forked from DaehwanKimLab/centrifuge
-
Notifications
You must be signed in to change notification settings - Fork 0
/
aligner_bt.cpp
1773 lines (1749 loc) · 54.1 KB
/
aligner_bt.cpp
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 2011, Ben Langmead <[email protected]>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 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.
*
* Bowtie 2 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 Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
*/
#include "aligner_bt.h"
#include "mask.h"
using namespace std;
#define CHECK_ROW_COL(rowc, colc) \ //这是多行宏 用于预编译时的替换
if(rowc >= 0 && colc >= 0) { \
if(!sawcell_[colc].insert(rowc)) { \ //
/* was already in there */ \
abort = true; \
return; \
} \
assert(local || prob_.cper_->debugCell(rowc, colc, hefc)); \ //成员访问运算符 用于引用类、结构和共用体的成员。
}
/**
* Fill in a triangle of the DP table and backtrace from the given cell to
* a cell in the previous checkpoint, or to the terminal cell.
*/
void BtBranchTracer::triangleFill( // :: 域操作符 用于在类外定义成员函数
int64_t rw, // row of cell to backtrace from //
int64_t cl, // column of cell to backtrace from
int hef, // cell to backtrace from is H (0), E (1), or F (2)
TAlScore targ, // score of cell to backtrace from
TAlScore targ_final, // score of alignment we're looking for
RandomSource& rnd, // pseudo-random generator //引用
int64_t& row_new, // out: row we ended up in after backtrace
int64_t& col_new, // out: column we ended up in after backtrace
int& hef_new, // out: H/E/F after backtrace
TAlScore& targ_new, // out: score up to cell we ended up in
bool& done, // out: finished tracing out an alignment?
bool& abort) // out: aborted b/c cell was seen before?
{
assert_geq(rw, 0);
assert_geq(cl, 0);
assert_range(0, 2, hef);
assert_lt(rw, (int64_t)prob_.qrylen_);
assert_lt(cl, (int64_t)prob_.reflen_);
assert(prob_.usecp_ && prob_.fill_);
int64_t row = rw, col = cl;
const int64_t colmin = 0;
const int64_t rowmin = 0;
const int64_t colmax = prob_.reflen_ - 1;
const int64_t rowmax = prob_.qrylen_ - 1;
assert_leq(prob_.reflen_, (TRefOff)sawcell_.size());
assert_leq(col, (int64_t)prob_.cper_->hicol());
assert_geq(col, (int64_t)prob_.cper_->locol());
assert_geq(prob_.cper_->per(), 2);
size_t mod = (row + col) & prob_.cper_->lomask(); // 位运算（整型） 或者 逻辑运算（布尔型）
assert_lt(mod, prob_.cper_->per());
// Allocate room for diags
size_t depth = mod+1;
assert_leq(depth, prob_.cper_->per());
size_t breadth = depth;
tri_.resize(depth);
// Allocate room for each diag
for(size_t i = 0; i < depth; i++) {
tri_[i].resize(breadth - i);
}
bool upperleft = false;
size_t off = (row + col) >> prob_.cper_->perpow2(); //二进制右移运算符。左操作数的值向右移动右操作数指定的位数。
if(off == 0) {
upperleft = true;
} else {
off--;
}
const TAlScore sc_rdo = prob_.sc_->readGapOpen(); //常类型的变量或对象的值是不能被更新的
const TAlScore sc_rde = prob_.sc_->readGapExtend();
const TAlScore sc_rfo = prob_.sc_->refGapOpen();
const TAlScore sc_rfe = prob_.sc_->refGapExtend();
const bool local = !prob_.sc_->monotone;
int64_t row_lo = row - (int64_t)mod;
const CpQuad *prev2 = NULL, *prev1 = NULL; //CpQuad是自定义的数据类型
if(!upperleft) {
// Read-only pointer to cells in diagonal -2. Start one row above the
// target row.
prev2 = prob_.cper_->qdiag1sPtr() + (off * prob_.cper_->nrow() + row_lo - 1);
// Read-only pointer to cells in diagonal -1. Start one row above the
// target row
prev1 = prob_.cper_->qdiag2sPtr() + (off * prob_.cper_->nrow() + row_lo - 1);
#ifndef NDEBUG
if(row >= (int64_t)mod) {
size_t rowc = row - mod, colc = col;
if(rowc > 0 && prob_.cper_->isCheckpointed(rowc-1, colc)) {
TAlScore al = prev1[0].sc[0];
if(al == MIN_I16) al = MIN_I64;
assert_eq(prob_.cper_->scoreTriangle(rowc-1, colc, 0), al);
}
if(rowc > 0 && colc > 0 && prob_.cper_->isCheckpointed(rowc-1, colc-1)) {
TAlScore al = prev2[0].sc[0];
if(al == MIN_I16) al = MIN_I64;
assert_eq(prob_.cper_->scoreTriangle(rowc-1, colc-1, 0), al);
}
}
#endif
}
// Pointer to cells in current diagonal
// For each diagonal we need to fill in
for(size_t i = 0; i < depth; i++) {
CpQuad * cur = tri_[i].ptr();
CpQuad * curc = cur;
size_t doff = mod - i; // # diagonals we are away from target diag
//assert_geq(row, (int64_t)doff);
int64_t rowc = row - doff;
int64_t colc = col;
size_t neval = 0; // # cells evaluated in this diag
ASSERT_ONLY(const CpQuad *last = NULL);
// Fill this diagonal from upper right to lower left
for(size_t j = 0; j < breadth; j++) {
if(rowc >= rowmin && rowc <= rowmax &&
colc >= colmin && colc <= colmax)
{
neval++;
int64_t fromend = prob_.qrylen_ - rowc - 1;
bool allowGaps = fromend >= prob_.sc_->gapbar && rowc >= prob_.sc_->gapbar;
// Fill this cell
// Some things we might want to calculate about this cell up front:
// 1. How many matches are possible from this cell to the cell in
// row, col, in case this allows us to prune
// Get character from read
int qc = prob_.qry_[rowc];
// Get quality value from read
int qq = prob_.qual_[rowc];
assert_geq(qq, 33);
// Get character from reference
int rc = prob_.ref_[colc];
assert_range(0, 16, rc);
int16_t sc_diag = prob_.sc_->score(qc, rc, qq - 33);
int16_t sc_h_up = MIN_I16;
int16_t sc_f_up = MIN_I16;
int16_t sc_h_lf = MIN_I16;
int16_t sc_e_lf = MIN_I16;
if(allowGaps) {
if(rowc > 0) {
assert(local || prev1[j+0].sc[2] < 0); //若条件返回错误，则终止程序执行
if(prev1[j+0].sc[0] > MIN_I16) {
sc_h_up = prev1[j+0].sc[0] - sc_rfo;
if(local) sc_h_up = max<int16_t>(sc_h_up, 0);
}
if(prev1[j+0].sc[2] > MIN_I16) {
sc_f_up = prev1[j+0].sc[2] - sc_rfe;
if(local) sc_f_up = max<int16_t>(sc_f_up, 0); //
}
#ifndef NDEBUG
TAlScore hup = prev1[j+0].sc[0];
TAlScore fup = prev1[j+0].sc[2];
if(hup == MIN_I16) hup = MIN_I64;
if(fup == MIN_I16) fup = MIN_I64;
if(local) {
hup = max<int16_t>(hup, 0);
fup = max<int16_t>(fup, 0);
}
if(prob_.cper_->isCheckpointed(rowc-1, colc)) {
assert_eq(hup, prob_.cper_->scoreTriangle(rowc-1, colc, 0));
assert_eq(fup, prob_.cper_->scoreTriangle(rowc-1, colc, 2));
}
#endif
}
if(colc > 0) {
assert(local || prev1[j+1].sc[1] < 0);
if(prev1[j+1].sc[0] > MIN_I16) {
sc_h_lf = prev1[j+1].sc[0] - sc_rdo;
if(local) sc_h_lf = max<int16_t>(sc_h_lf, 0);
}
if(prev1[j+1].sc[1] > MIN_I16) {
sc_e_lf = prev1[j+1].sc[1] - sc_rde;
if(local) sc_e_lf = max<int16_t>(sc_e_lf, 0);
}
#ifndef NDEBUG
TAlScore hlf = prev1[j+1].sc[0];
TAlScore elf = prev1[j+1].sc[1];
if(hlf == MIN_I16) hlf = MIN_I64;
if(elf == MIN_I16) elf = MIN_I64;
if(local) {
hlf = max<int16_t>(hlf, 0);
elf = max<int16_t>(elf, 0);
}
if(prob_.cper_->isCheckpointed(rowc, colc-1)) {
assert_eq(hlf, prob_.cper_->scoreTriangle(rowc, colc-1, 0));
assert_eq(elf, prob_.cper_->scoreTriangle(rowc, colc-1, 1));
}
#endif
}
}
assert(rowc <= 1 || colc <= 0 || prev2 != NULL);
int16_t sc_h_dg = ((rowc > 0 && colc > 0) ? prev2[j+0].sc[0] : 0);
if(colc == 0 && rowc > 0 && !local) {
sc_h_dg = MIN_I16;
}
if(sc_h_dg > MIN_I16) {
sc_h_dg += sc_diag;
}
if(local) sc_h_dg = max<int16_t>(sc_h_dg, 0);
// cerr << sc_diag << " " << sc_h_dg << " " << sc_h_up << " " << sc_f_up << " " << sc_h_lf << " " << sc_e_lf << endl;
int mask = 0;
// Calculate best ways into H, E, F cells starting with H.
// Mask bits:
// H: 1=diag, 2=hhoriz, 4=ehoriz, 8=hvert, 16=fvert
// E: 32=hhoriz, 64=ehoriz
// F: 128=hvert, 256=fvert
int16_t sc_best = sc_h_dg;
if(sc_h_dg > MIN_I64) {
mask = 1;
}
if(colc > 0 && sc_h_lf >= sc_best && sc_h_lf > MIN_I64) {
if(sc_h_lf > sc_best) mask = 0;
mask |= 2; // 二进制位运算 二者取或
sc_best = sc_h_lf;
}
if(colc > 0 && sc_e_lf >= sc_best && sc_e_lf > MIN_I64) {
if(sc_e_lf > sc_best) mask = 0;
mask |= 4;
sc_best = sc_e_lf;
}
if(rowc > 0 && sc_h_up >= sc_best && sc_h_up > MIN_I64) {
if(sc_h_up > sc_best) mask = 0;
mask |= 8;
sc_best = sc_h_up;
}
if(rowc > 0 && sc_f_up >= sc_best && sc_f_up > MIN_I64) {
if(sc_f_up > sc_best) mask = 0;
mask |= 16;
sc_best = sc_f_up;
}
// Calculate best way into E cell
int16_t sc_e_best = sc_h_lf;
if(colc > 0) {
if(sc_h_lf >= sc_e_lf && sc_h_lf > MIN_I64) {
if(sc_h_lf == sc_e_lf) {
mask |= 64;
}
mask |= 32;
} else if(sc_e_lf > MIN_I64) {
sc_e_best = sc_e_lf;
mask |= 64;
}
}
if(sc_e_best > sc_best) {
sc_best = sc_e_best;
mask &= ~31; // don't go diagonal
}
// Calculate best way into F cell
int16_t sc_f_best = sc_h_up;
if(rowc > 0) {
if(sc_h_up >= sc_f_up && sc_h_up > MIN_I64) {
if(sc_h_up == sc_f_up) {
mask |= 256;
}
mask |= 128;
} else if(sc_f_up > MIN_I64) {
sc_f_best = sc_f_up;
mask |= 256;
}
}
if(sc_f_best > sc_best) {
sc_best = sc_f_best;
mask &= ~127; // don't go horizontal or diagonal 二进制补码运算符，具有翻转位效果。
}
// Install results in cur
assert(!prob_.sc_->monotone || sc_best <= 0);
assert(!prob_.sc_->monotone || sc_e_best <= 0);
assert(!prob_.sc_->monotone || sc_f_best <= 0);
curc->sc[0] = sc_best;
assert( local || sc_e_best < 0);
assert( local || sc_f_best < 0);
assert(!local || sc_e_best >= 0 || sc_e_best == MIN_I16);
assert(!local || sc_f_best >= 0 || sc_f_best == MIN_I16);
curc->sc[1] = sc_e_best;
curc->sc[2] = sc_f_best;
curc->sc[3] = mask;
// cerr << curc->sc[0] << " " << curc->sc[1] << " " << curc->sc[2] << " " << curc->sc[3] << endl;
ASSERT_ONLY(last = curc);
#ifndef NDEBUG
if(prob_.cper_->isCheckpointed(rowc, colc)) {
if(local) {
sc_e_best = max<int16_t>(sc_e_best, 0);
sc_f_best = max<int16_t>(sc_f_best, 0);
}
TAlScore sc_best64 = sc_best; if(sc_best == MIN_I16) sc_best64 = MIN_I64;
TAlScore sc_e_best64 = sc_e_best; if(sc_e_best == MIN_I16) sc_e_best64 = MIN_I64;
TAlScore sc_f_best64 = sc_f_best; if(sc_f_best == MIN_I16) sc_f_best64 = MIN_I64;
assert_eq(prob_.cper_->scoreTriangle(rowc, colc, 0), sc_best64);
assert_eq(prob_.cper_->scoreTriangle(rowc, colc, 1), sc_e_best64);
assert_eq(prob_.cper_->scoreTriangle(rowc, colc, 2), sc_f_best64);
}
#endif
}
// Update row, col
assert_lt(rowc, (int64_t)prob_.qrylen_);
rowc++;
colc--;
curc++;
} // for(size_t j = 0; j < breadth; j++)
if(i == depth-1) {
// Final iteration
assert(last != NULL);
assert_eq(1, neval);
assert_neq(0, last->sc[3]);
assert_eq(targ, last->sc[hef]);
} else {
breadth--;
prev2 = prev1 + 1;
prev1 = cur;
}
} // for(size_t i = 0; i < depth; i++)
//
// Now backtrack through the triangle. Abort as soon as we enter a cell
// that was visited by a previous backtrace.
//
int64_t rowc = row, colc = col;
size_t curid;
int hefc = hef;
if(bs_.empty()) {
// Start an initial branch
CHECK_ROW_COL(rowc, colc); //调用宏
curid = bs_.alloc(); //
assert_eq(0, curid);
Edit e;
bs_[curid].init(
prob_,
0, // parent ID
0, // penalty
0, // score_en
rowc, // row
colc, // col
e, // edit
0, // hef
true, // I am the root
false); // don't try to extend with exact matches
bs_[curid].len_ = 0;
} else {
curid = bs_.size()-1;
}
size_t idx_orig = (row + col) >> prob_.cper_->perpow2(); //二进制右移运算符
while(true) {
// What depth are we?
size_t mod = (rowc + colc) & prob_.cper_->lomask(); //二进制 AND 运算符
assert_lt(mod, prob_.cper_->per());
CpQuad * cur = tri_[mod].ptr(); //是指针么？？
int64_t row_off = rowc - row_lo - mod;
assert(!local || cur[row_off].sc[0] > 0);
assert_geq(row_off, 0);
int mask = cur[row_off].sc[3];
assert_gt(mask, 0);
int sel = -1;
// Select what type of move to make, which depends on whether we're
// currently in H, E, F:
if(hefc == 0) {
if( (mask & 1) != 0) { //二进制 AND 运算符
// diagonal
sel = 0;
} else if((mask & 8) != 0) {
// up to H
sel = 3;
} else if((mask & 16) != 0) {
// up to F
sel = 4;
} else if((mask & 2) != 0) {
// left to H
sel = 1;
} else if((mask & 4) != 0) {
// left to E
sel = 2;
}
} else if(hefc == 1) {
if( (mask & 32) != 0) {
// left to H
sel = 5;
} else if((mask & 64) != 0) {
// left to E
sel = 6;
}
} else {
assert_eq(2, hefc);
if( (mask & 128) != 0) {
// up to H
sel = 7;
} else if((mask & 256) != 0) {
// up to F
sel = 8;
}
}
assert_geq(sel, 0);
// Get character from read
int qc = prob_.qry_[rowc], qq = prob_.qual_[rowc];
// Get character from reference
int rc = prob_.ref_[colc];
assert_range(0, 16, rc);
// Now that we know what type of move to make, make it, updating our
// row and column and moving updating the branch.
if(sel == 0) {
assert_geq(rowc, 0);
assert_geq(colc, 0);
TAlScore scd = prob_.sc_->score(qc, rc, qq - 33);
if((rc & (1 << qc)) == 0) { //
// Mismatch
size_t id = curid;
// Check if the previous branch was the initial (bottommost)
// branch with no matches. If so, the mismatch should be added
// to the initial branch, instead of starting a new branch.
bool empty = (bs_[curid].len_ == 0 && curid == 0); //布尔型
if(!empty) {
id = bs_.alloc();
}
Edit e((int)rowc, mask2dna[rc], "ACGTN"[qc], EDIT_TYPE_MM); //(int)强制转换成int
assert_lt(scd, 0);
TAlScore score_en = bs_[curid].score_st_ + scd;
bs_[id].init(
prob_,
curid, // parent ID
-scd, // penalty
score_en, // score_en
rowc, // row
colc, // col
e, // edit
hefc, // hef
empty, // root?
false); // don't try to extend with exact matches
//assert(!local || bs_[id].score_st_ >= 0);
curid = id;
} else {
// Match
bs_[curid].score_st_ += prob_.sc_->match();
bs_[curid].len_++;
assert_leq((int64_t)bs_[curid].len_, bs_[curid].row_ + 1); //强制转化成int64_t
}
rowc--;
colc--;
assert(local || bs_[curid].score_st_ >= targ_final);
hefc = 0;
} else if((sel >= 1 && sel <= 2) || (sel >= 5 && sel <= 6)) {
assert_gt(colc, 0);
// Read gap
size_t id = bs_.alloc();
Edit e((int)rowc+1, mask2dna[rc], '-', EDIT_TYPE_READ_GAP);
TAlScore gapp = prob_.sc_->readGapOpen();
if(bs_[curid].len_ == 0 && bs_[curid].e_.inited() && bs_[curid].e_.isReadGap()) {
gapp = prob_.sc_->readGapExtend();
}
TAlScore score_en = bs_[curid].score_st_ - gapp;
bs_[id].init(
prob_,
curid, // parent ID
gapp, // penalty
score_en, // score_en
rowc, // row
colc-1, // col
e, // edit
hefc, // hef
false, // root?
false); // don't try to extend with exact matches
colc--;
curid = id;
assert( local || bs_[curid].score_st_ >= targ_final);
//assert(!local || bs_[curid].score_st_ >= 0);
if(sel == 1 || sel == 5) {
hefc = 0;
} else {
hefc = 1;
}
} else {
assert_gt(rowc, 0);
// Reference gap
size_t id = bs_.alloc();
Edit e((int)rowc, '-', "ACGTN"[qc], EDIT_TYPE_REF_GAP);
TAlScore gapp = prob_.sc_->refGapOpen();
if(bs_[curid].len_ == 0 && bs_[curid].e_.inited() && bs_[curid].e_.isRefGap()) {
gapp = prob_.sc_->refGapExtend();
}
TAlScore score_en = bs_[curid].score_st_ - gapp;
bs_[id].init(
prob_,
curid, // parent ID
gapp, // penalty
score_en, // score_en
rowc-1, // row
colc, // col
e, // edit
hefc, // hef
false, // root?
false); // don't try to extend with exact matches
rowc--;
curid = id;
//assert(!local || bs_[curid].score_st_ >= 0);
if(sel == 3 || sel == 7) {
hefc = 0;
} else {
hefc = 2;
}
}
CHECK_ROW_COL(rowc, colc); //宏替换
size_t mod_new = (rowc + colc) & prob_.cper_->lomask(); //二进制 AND 运算符
size_t idx = (rowc + colc) >> prob_.cper_->perpow2(); //二进制右移运算符
assert_lt(mod_new, prob_.cper_->per());
int64_t row_off_new = rowc - row_lo - mod_new;
CpQuad * cur_new = NULL; //
if(colc >= 0 && rowc >= 0 && idx == idx_orig) {
cur_new = tri_[mod_new].ptr();
}
bool hit_new_tri = (idx < idx_orig && colc >= 0 && rowc >= 0);
// Check whether we made it to the top row or to a cell with score 0
if(colc < 0 || rowc < 0 ||
(cur_new != NULL && (local && cur_new[row_off_new].sc[0] == 0)))
{
done = true;
assert(bs_[curid].isSolution(prob_));
addSolution(curid);
#ifndef NDEBUG
// A check to see if any two adjacent branches in the backtrace
// overlap. If they do, the whole alignment will be filtered out
// in trySolution(...)
size_t cur = curid;
if(!bs_[cur].root_) {
size_t next = bs_[cur].parentId_;
while(!bs_[next].root_) {
assert_neq(cur, next);
if(bs_[next].len_ != 0 || bs_[cur].len_ == 0) {
assert(!bs_[cur].overlap(prob_, bs_[next]));
}
cur = next;
next = bs_[cur].parentId_;
}
}
#endif
return;
}
if(hit_new_tri) {
assert(rowc < 0 || colc < 0 || prob_.cper_->isCheckpointed(rowc, colc));
row_new = rowc; col_new = colc;
hef_new = hefc;
done = false;
if(rowc < 0 || colc < 0) {
assert(local);
targ_new = 0;
} else {
targ_new = prob_.cper_->scoreTriangle(rowc, colc, hefc);
}
if(local && targ_new == 0) {
done = true;
assert(bs_[curid].isSolution(prob_));
addSolution(curid);
}
assert((row_new >= 0 && col_new >= 0) || done);
return;
}
}
assert(false);
}
#ifndef NDEBUG //条件编译
#define DEBUG_CHECK(ss, row, col, hef) { \
if(prob_.cper_->debug() && row >= 0 && col >= 0) { \
TAlScore s = ss; \
if(s == MIN_I16) s = MIN_I64; \
if(local && s < 0) s = 0; \
TAlScore deb = prob_.cper_->debugCell(row, col, hef); \
if(local && deb < 0) deb = 0; \
assert_eq(s, deb); \
} \
}
#else
#define DEBUG_CHECK(ss, row, col, hef)
#endif
/**
* Fill in a square of the DP table and backtrace from the given cell to
* a cell in the previous checkpoint, or to the terminal cell.
*/
void BtBranchTracer::squareFill( //在类外定义函数
int64_t rw, // row of cell to backtrace from
int64_t cl, // column of cell to backtrace from
int hef, // cell to backtrace from is H (0), E (1), or F (2)
TAlScore targ, // score of cell to backtrace from
TAlScore targ_final, // score of alignment we're looking for
RandomSource& rnd, // pseudo-random generator
int64_t& row_new, // out: row we ended up in after backtrace
int64_t& col_new, // out: column we ended up in after backtrace
int& hef_new, // out: H/E/F after backtrace
TAlScore& targ_new, // out: score up to cell we ended up in
bool& done, // out: finished tracing out an alignment?
bool& abort) // out: aborted b/c cell was seen before?
{
assert_geq(rw, 0);
assert_geq(cl, 0);
assert_range(0, 2, hef);
assert_lt(rw, (int64_t)prob_.qrylen_); //强制转换
assert_lt(cl, (int64_t)prob_.reflen_);
assert(prob_.usecp_ && prob_.fill_);
const bool is8_ = prob_.cper_->is8_;
int64_t row = rw, col = cl;
assert_leq(prob_.reflen_, (TRefOff)sawcell_.size()); //强制转换
assert_leq(col, (int64_t)prob_.cper_->hicol());
assert_geq(col, (int64_t)prob_.cper_->locol());
assert_geq(prob_.cper_->per(), 2);
size_t xmod = col & prob_.cper_->lomask();
size_t ymod = row & prob_.cper_->lomask();
size_t xdiv = col >> prob_.cper_->perpow2();
size_t ydiv = row >> prob_.cper_->perpow2();
size_t sq_ncol = xmod+1, sq_nrow = ymod+1;
sq_.resize(sq_ncol * sq_nrow);
bool upper = ydiv == 0;
bool left = xdiv == 0;
const TAlScore sc_rdo = prob_.sc_->readGapOpen();
const TAlScore sc_rde = prob_.sc_->readGapExtend();
const TAlScore sc_rfo = prob_.sc_->refGapOpen();
const TAlScore sc_rfe = prob_.sc_->refGapExtend();
const bool local = !prob_.sc_->monotone;
const CpQuad *qup = NULL; //指针
const __m128i *qlf = NULL;
size_t per = prob_.cper_->per_;
ASSERT_ONLY(size_t nrow = prob_.cper_->nrow());
size_t ncol = prob_.cper_->ncol();
assert_eq(prob_.qrylen_, nrow);
assert_eq(prob_.reflen_, (TRefOff)ncol);
size_t niter = prob_.cper_->niter_;
if(!upper) {
qup = prob_.cper_->qrows_.ptr() + (ncol * (ydiv-1)) + xdiv * per;
}
if(!left) {
// Set up the column pointers to point to the first __m128i word in the
// relevant column
size_t off = (niter << 2) * (xdiv-1); //二进制左移运算符
qlf = prob_.cper_->qcols_.ptr() + off;
}
size_t xedge = xdiv * per; // absolute offset of leftmost cell in square
size_t yedge = ydiv * per; // absolute offset of topmost cell in square
size_t xi = xedge, yi = yedge; // iterators for columns, rows
size_t ii = 0; // iterator into packed square
// Iterate over rows, then over columns
size_t m128mod = yi % prob_.cper_->niter_;
size_t m128div = yi / prob_.cper_->niter_;
int16_t sc_h_dg_lastrow = MIN_I16;
for(size_t i = 0; i <= ymod; i++, yi++) {
assert_lt(yi, nrow);
xi = xedge;
// Handling for first column is done outside the loop
size_t fromend = prob_.qrylen_ - yi - 1;
bool allowGaps = fromend >= (size_t)prob_.sc_->gapbar && yi >= (size_t)prob_.sc_->gapbar;
// Get character, quality from read
int qc = prob_.qry_[yi], qq = prob_.qual_[yi];
assert_geq(qq, 33);
int16_t sc_h_lf_last = MIN_I16;
int16_t sc_e_lf_last = MIN_I16;
for(size_t j = 0; j <= xmod; j++, xi++) {
assert_lt(xi, ncol);
// Get character from reference
int rc = prob_.ref_[xi];
assert_range(0, 16, rc);
int16_t sc_diag = prob_.sc_->score(qc, rc, qq - 33);
int16_t sc_h_up = MIN_I16, sc_f_up = MIN_I16,
sc_h_lf = MIN_I16, sc_e_lf = MIN_I16,
sc_h_dg = MIN_I16;
int16_t sc_h_up_c = MIN_I16, sc_f_up_c = MIN_I16,
sc_h_lf_c = MIN_I16, sc_e_lf_c = MIN_I16,
sc_h_dg_c = MIN_I16;
if(yi == 0) {
// If I'm in the first first row or column set it to 0
sc_h_dg = 0;
} else if(xi == 0) {
// Do nothing; leave it at min
if(local) {
sc_h_dg = 0;
}
} else if(i == 0 && j == 0) {
// Otherwise, if I'm in the upper-left square corner, I can get
// it from the checkpoint
sc_h_dg = qup[-1].sc[0]; //数组索引值为负？
} else if(j == 0) {
// Otherwise, if I'm in the leftmost cell of this row, I can
// get it from sc_h_lf in first column of previous row
sc_h_dg = sc_h_dg_lastrow;
} else {
// Otherwise, I can get it from qup
sc_h_dg = qup[j-1].sc[0];
}
if(yi > 0 && xi > 0) DEBUG_CHECK(sc_h_dg, yi-1, xi-1, 2);
// If we're in the leftmost column, calculate sc_h_lf regardless of
// allowGaps.
if(j == 0 && xi > 0) {
// Get values for left neighbors from the checkpoint
if(is8_) {
size_t vecoff = (m128mod << 6) + m128div; //二进制左移运算符
sc_e_lf = ((uint8_t*)(qlf + 0))[vecoff];
sc_h_lf = ((uint8_t*)(qlf + 2))[vecoff];
if(local) {
// No adjustment
} else {
if(sc_h_lf == 0) sc_h_lf = MIN_I16;
else sc_h_lf -= 0xff; // 十六进制 255
if(sc_e_lf == 0) sc_e_lf = MIN_I16;
else sc_e_lf -= 0xff;
}
} else {
size_t vecoff = (m128mod << 5) + m128div; //二进制左移运算符
sc_e_lf = ((int16_t*)(qlf + 0))[vecoff];
sc_h_lf = ((int16_t*)(qlf + 2))[vecoff];
if(local) {
sc_h_lf += 0x8000; assert_geq(sc_h_lf, 0); //十六进制 32768
sc_e_lf += 0x8000; assert_geq(sc_e_lf, 0);
} else {
if(sc_h_lf != MIN_I16) sc_h_lf -= 0x7fff; //十六进制 32767
if(sc_e_lf != MIN_I16) sc_e_lf -= 0x7fff;
}
}
DEBUG_CHECK(sc_e_lf, yi, xi-1, 0);
DEBUG_CHECK(sc_h_lf, yi, xi-1, 2);
sc_h_dg_lastrow = sc_h_lf;
}
if(allowGaps) {
if(j == 0 /* at left edge */ && xi > 0 /* not extreme */) {
sc_h_lf_c = sc_h_lf;
sc_e_lf_c = sc_e_lf;
if(sc_h_lf_c != MIN_I16) sc_h_lf_c -= sc_rdo;
if(sc_e_lf_c != MIN_I16) sc_e_lf_c -= sc_rde;
assert_leq(sc_h_lf_c, prob_.cper_->perf_);
assert_leq(sc_e_lf_c, prob_.cper_->perf_); //-> 指向结构体成员运算符
} else if(xi > 0) {
// Get values for left neighbors from the previous iteration
if(sc_h_lf_last != MIN_I16) {
sc_h_lf = sc_h_lf_last;
sc_h_lf_c = sc_h_lf - sc_rdo;
}
if(sc_e_lf_last != MIN_I16) {
sc_e_lf = sc_e_lf_last;
sc_e_lf_c = sc_e_lf - sc_rde;
}
}
if(yi > 0 /* not extreme */) {
// Get column values
assert(qup != NULL);
assert(local || qup[j].sc[2] < 0);
if(qup[j].sc[0] > MIN_I16) {
DEBUG_CHECK(qup[j].sc[0], yi-1, xi, 2);
sc_h_up = qup[j].sc[0];
sc_h_up_c = sc_h_up - sc_rfo;
}
if(qup[j].sc[2] > MIN_I16) {
DEBUG_CHECK(qup[j].sc[2], yi-1, xi, 1);
sc_f_up = qup[j].sc[2]; //结构体成员操作符
sc_f_up_c = sc_f_up - sc_rfe;
}
}
if(local) {
sc_h_up_c = max<int16_t>(sc_h_up_c, 0);
sc_f_up_c = max<int16_t>(sc_f_up_c, 0);
sc_h_lf_c = max<int16_t>(sc_h_lf_c, 0);
sc_e_lf_c = max<int16_t>(sc_e_lf_c, 0);
}
}
if(sc_h_dg > MIN_I16) {
sc_h_dg_c = sc_h_dg + sc_diag;
}
if(local) sc_h_dg_c = max<int16_t>(sc_h_dg_c, 0);
int mask = 0;
// Calculate best ways into H, E, F cells starting with H.
// Mask bits:
// H: 1=diag, 2=hhoriz, 4=ehoriz, 8=hvert, 16=fvert
// E: 32=hhoriz, 64=ehoriz
// F: 128=hvert, 256=fvert
int16_t sc_best = sc_h_dg_c;
if(sc_h_dg_c > MIN_I64) {
mask = 1;
}
if(xi > 0 && sc_h_lf_c >= sc_best && sc_h_lf_c > MIN_I64) {
if(sc_h_lf_c > sc_best) mask = 0;
mask |= 2;
sc_best = sc_h_lf_c;
}
if(xi > 0 && sc_e_lf_c >= sc_best && sc_e_lf_c > MIN_I64) {
if(sc_e_lf_c > sc_best) mask = 0;
mask |= 4;
sc_best = sc_e_lf_c;
}
if(yi > 0 && sc_h_up_c >= sc_best && sc_h_up_c > MIN_I64) {
if(sc_h_up_c > sc_best) mask = 0;
mask |= 8;
sc_best = sc_h_up_c;
}
if(yi > 0 && sc_f_up_c >= sc_best && sc_f_up_c > MIN_I64) {
if(sc_f_up_c > sc_best) mask = 0;
mask |= 16;
sc_best = sc_f_up_c;
}
// Calculate best way into E cell
int16_t sc_e_best = sc_h_lf_c;
if(xi > 0) {
if(sc_h_lf_c >= sc_e_lf_c && sc_h_lf_c > MIN_I64) {
if(sc_h_lf_c == sc_e_lf_c) {
mask |= 64;
}
mask |= 32;
} else if(sc_e_lf_c > MIN_I64) {
sc_e_best = sc_e_lf_c;
mask |= 64;
}
}
if(sc_e_best > sc_best) {
sc_best = sc_e_best;
mask &= ~31; // don't go diagonal 按位取非
}
// Calculate best way into F cell
int16_t sc_f_best = sc_h_up_c;
if(yi > 0) {
if(sc_h_up_c >= sc_f_up_c && sc_h_up_c > MIN_I64) {
if(sc_h_up_c == sc_f_up_c) {
mask |= 256;
}
mask |= 128;
} else if(sc_f_up_c > MIN_I64) {
sc_f_best = sc_f_up_c;
mask |= 256;
}
}
if(sc_f_best > sc_best) {
sc_best = sc_f_best;
mask &= ~127; // don't go horizontal or diagonal
}
// Install results in cur
assert( local || sc_best <= 0);
sq_[ii+j].sc[0] = sc_best;
assert( local || sc_e_best < 0);
assert( local || sc_f_best < 0);
assert(!local || sc_e_best >= 0 || sc_e_best == MIN_I16);
assert(!local || sc_f_best >= 0 || sc_f_best == MIN_I16);
sq_[ii+j].sc[1] = sc_e_best;
sq_[ii+j].sc[2] = sc_f_best;
sq_[ii+j].sc[3] = mask;
DEBUG_CHECK(sq_[ii+j].sc[0], yi, xi, 2); // H
DEBUG_CHECK(sq_[ii+j].sc[1], yi, xi, 0); // E
DEBUG_CHECK(sq_[ii+j].sc[2], yi, xi, 1); // F
// Update sc_h_lf_last, sc_e_lf_last
sc_h_lf_last = sc_best;
sc_e_lf_last = sc_e_best;
}
// Update m128mod, m128div
m128mod++;
if(m128mod == prob_.cper_->niter_) {
m128mod = 0;
m128div++;
}
// update qup
ii += sq_ncol;
// dimensions of sq_
qup = sq_.ptr() + sq_ncol * i;
}
assert_eq(targ, sq_[ymod * sq_ncol + xmod].sc[hef]);
//
// Now backtrack through the triangle. Abort as soon as we enter a cell
// that was visited by a previous backtrace.
//
int64_t rowc = row, colc = col;
size_t curid;
int hefc = hef;
if(bs_.empty()) {
// Start an initial branch
CHECK_ROW_COL(rowc, colc);
curid = bs_.alloc();
assert_eq(0, curid);
Edit e;
bs_[curid].init(
prob_,
0, // parent ID
0, // penalty
0, // score_en
rowc, // row
colc, // col
e, // edit
0, // hef
true, // root?
false); // don't try to extend with exact matches
bs_[curid].len_ = 0;
} else {
curid = bs_.size()-1;
}
size_t ymodTimesNcol = ymod * sq_ncol;
while(true) {
// What depth are we?
assert_eq(ymodTimesNcol, ymod * sq_ncol);
CpQuad * cur = sq_.ptr() + ymodTimesNcol + xmod; //
int mask = cur->sc[3];
assert_gt(mask, 0);
int sel = -1;
// Select what type of move to make, which depends on whether we're
// currently in H, E, F:
if(hefc == 0) {
if( (mask & 1) != 0) { //位与运算
// diagonal
sel = 0;
} else if((mask & 8) != 0) {
// up to H
sel = 3;
} else if((mask & 16) != 0) {
// up to F
sel = 4;
} else if((mask & 2) != 0) {
// left to H
sel = 1;
} else if((mask & 4) != 0) {
// left to E
sel = 2;
}
} else if(hefc == 1) {
if( (mask & 32) != 0) {
// left to H
sel = 5;
} else if((mask & 64) != 0) {
// left to E
sel = 6;
}
} else {
assert_eq(2, hefc);
if( (mask & 128) != 0) {
// up to H
sel = 7;
} else if((mask & 256) != 0) {
// up to F
sel = 8;
}
}
assert_geq(sel, 0);
// Get character from read
int qc = prob_.qry_[rowc], qq = prob_.qual_[rowc];
// Get character from reference
int rc = prob_.ref_[colc];
assert_range(0, 16, rc);
bool xexit = false, yexit = false;
// Now that we know what type of move to make, make it, updating our
// row and column and moving updating the branch.
if(sel == 0) {
assert_geq(rowc, 0);
assert_geq(colc, 0);
TAlScore scd = prob_.sc_->score(qc, rc, qq - 33);
if((rc & (1 << qc)) == 0) {
// Mismatch
size_t id = curid;
// Check if the previous branch was the initial (bottommost)
// branch with no matches. If so, the mismatch should be added
// to the initial branch, instead of starting a new branch.
bool empty = (bs_[curid].len_ == 0 && curid == 0);
if(!empty) {
id = bs_.alloc();
}
Edit e((int)rowc, mask2dna[rc], "ACGTN"[qc], EDIT_TYPE_MM);
assert_lt(scd, 0);
TAlScore score_en = bs_[curid].score_st_ + scd;
bs_[id].init(
prob_,
curid, // parent ID
-scd, // penalty
score_en, // score_en
rowc, // row
colc, // col
e, // edit
hefc, // hef
empty, // root?
false); // don't try to extend with exact matches
curid = id;
//assert(!local || bs_[curid].score_st_ >= 0);
} else {
// Match
bs_[curid].score_st_ += prob_.sc_->match();
bs_[curid].len_++;
assert_leq((int64_t)bs_[curid].len_, bs_[curid].row_ + 1);
}
if(xmod == 0) xexit = true;
if(ymod == 0) yexit = true;
rowc--; ymod--; ymodTimesNcol -= sq_ncol;
colc--; xmod--;
assert(local || bs_[curid].score_st_ >= targ_final);
hefc = 0;
} else if((sel >= 1 && sel <= 2) || (sel >= 5 && sel <= 6)) {
assert_gt(colc, 0);
// Read gap
size_t id = bs_.alloc();
Edit e((int)rowc+1, mask2dna[rc], '-', EDIT_TYPE_READ_GAP);
TAlScore gapp = prob_.sc_->readGapOpen();