-
Notifications
You must be signed in to change notification settings - Fork 20
/
Copy pathyahs.c
1182 lines (1045 loc) · 44.3 KB
/
yahs.c
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
/*********************************************************************************
* MIT License *
* *
* Copyright (c) 2021 Chenxi Zhou <[email protected]> *
* *
* Permission is hereby granted, free of charge, to any person obtaining a copy *
* of this software and associated documentation files (the "Software"), to deal *
* in the Software without restriction, including without limitation the rights *
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell *
* copies of the Software, and to permit persons to whom the Software is *
* furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE *
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER *
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, *
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE *
* SOFTWARE. *
*********************************************************************************/
/********************************** Revision History *****************************
* *
* 22/06/21 - Chenxi Zhou: Created *
* *
*********************************************************************************/
#include <stdlib.h>
#include <stdio.h>
#include <assert.h>
#include <ctype.h>
#include <errno.h>
#include "ketopt.h"
#include "kvec.h"
#include "sdict.h"
#include "link.h"
#include "cov.h"
#include "graph.h"
#include "break.h"
#include "enzyme.h"
#include "telo.h"
#include "asset.h"
#include "version.h"
#undef DEBUG_ERROR_BREAK
#undef DEBUG_GRAPH_PRUNE
#undef DEBUG_OPTIONS
#undef DEBUG_RAM_USAGE
#undef DEBUG_QLF
#undef DEBUG_ENZ
#undef DEBUG_GT4G
#undef DEBUG_LINK
#define ENOMEM_ERR 15
#define ENOBND_ERR 14
#define GB 0x40000000
#define MAX_N_SEQ 45000
#ifndef DEBUG_GT4G
static int ec_min_window = 1000000;
static int ec_resolution = 10000;
static int ec_bin = 1000;
static int ec_move_avg = 0;
static int ec_merge_thresh = 10000;
static int ec_dual_break_thresh = 50000;
#else
static int ec_min_window = 5000000;
static int ec_resolution = 50000;
static int ec_bin = 5000;
static int ec_move_avg = 0;
static int ec_merge_thresh = 50000;
static int ec_dual_break_thresh = 250000;
#endif
static double ec_min_frac = .8;
static double ec_fold_thresh = .2;
static double max_noise_ratio = .1;
static int max_extra_try = 3;
static uint64_t n_stats[10];
static uint32_t l_stats[10];
double qbinom(double, double, double, int, int);
enum fileTypes{NOSET, BED, BAM, BIN, PA5};
int VERBOSE = 0;
static double ys_realtime0;
graph_t *build_graph_from_links(inter_link_mat_t *link_mat, asm_dict_t *dict, double min_norm, double la, int8_t *telo_ends)
{
int32_t i, j, n, c0, c1;
uint32_t v, w;
int8_t t;
double norm, qla;
inter_link_t *link;
graph_t *g;
graph_arc_t *arc;
g = graph_init();
g->sdict = dict;
// build graph
n = link_mat->n;
for (i = 0; i < n; ++i) {
link = &link_mat->links[i];
if (link->n == 0 || link->n0 == 0)
continue;
c0 = link->c0;
c1 = link->c1;
t = link->linkt;
if (!t)
continue;
qla = qbinom(.99, link->n0, la, 1, 0) / link->n0;
for (j = 0; j < 4; ++j) {
if (1 << j & t) {
norm = link->norms[j];
if (norm >= min_norm) {
if (norm < qla) {
#ifdef DEBUG_QLF
fprintf(stderr, "[DEBUG_QLF::%s] #Edge rejected by QL filter: %s %s %u %u %.3f (< %.3f)\n", __func__, dict->s[c0].name, dict->s[c1].name, j, link->n0, norm, qla);
#endif
continue;
}
v = c0<<1 | (j>>1);
w = c1<<1 | (j&1);
if (telo_ends[v^1] || telo_ends[w])
continue;
arc = graph_add_arc(g, v, w, -1, 0, norm);
graph_add_arc(g, w^1, v^1, arc->link_id, 0, norm);
}
}
}
}
graph_arc_sort(g);
graph_arc_index(g);
return g;
}
#define MAX_TELO_CLIP 50
int8_t *find_aseq_telos(asm_dict_t *dict, int8_t *telo_ends)
{
int i, n;
int8_t *telos;
sdict_t *sdict;
sd_aseq_t *aseq;
sd_seg_t *segs, *seg;
sdict = dict->sdict;
n = dict->n;
telos = (int8_t *) calloc(dict->n * 2, sizeof(int8_t));
segs = dict->seg;
for (i = 0; i < n; i++) {
aseq = &dict->s[i];
// first seg
seg = &segs[aseq->s];
if ((telo_ends[seg->c>>1<<1] && seg->x <= MAX_TELO_CLIP && (seg->c&1) == 0) ||
(telo_ends[seg->c>>1<<1|1] && (seg->x + seg->y + MAX_TELO_CLIP) >= sdict->s[seg->c>>1].len && (seg->c&1) == 1))
telos[i<<1] = 1;
// last seg
seg = &segs[aseq->s + aseq->n - 1];
if ((telo_ends[seg->c>>1<<1] && seg->x <= MAX_TELO_CLIP && (seg->c&1) == 1) ||
(telo_ends[seg->c>>1<<1|1] && (seg->x + seg->y + MAX_TELO_CLIP) >= sdict->s[seg->c>>1].len && (seg->c&1) == 0))
telos[i<<1|1] = 1;
}
return telos;
}
int run_scaffolding(char *fai, char *agp, char *link_file, cov_norm_t *cov_norm, uint32_t ml, uint8_t mq, re_cuts_t *re_cuts, int8_t *telo_ends, char *out, int resolution, double *noise, uint32_t d_min_cell, double d_mass_frac, long rss_limit, int no_mem_check)
{
//TODO: adjust wt thres by resolution
sdict_t *sdict = make_sdict_from_index(fai, ml);
asm_dict_t *dict = agp? make_asm_dict_from_agp(sdict, agp, 1) : make_asm_dict_from_sdict(sdict);
int i, re = 0;
uint64_t len = 0;
for (i = 0; i < dict->n; ++i)
len += dict->s[i].len;
#ifdef DEBUG_GRAPH_PRUNE
fprintf(stderr, "[DEBUG_GRAPH_PRUNE::%s] #sequences loaded %d = %lubp\n", __func__, dict->n, len);
#endif
long rss_intra, rss_inter;
rss_intra = no_mem_check? 0 : estimate_intra_link_mat_init_rss(dict, resolution, 1);
if ((rss_limit >= 0 && rss_intra > rss_limit) || rss_intra < 0) {
// no enough memory
fprintf(stderr, "[I::%s] No enough memory. Try lower resolutions... End of scaffolding round.\n", __func__);
fprintf(stderr, "[I::%s] RAM limit: %.3fGB\n", __func__, (double) rss_limit / GB);
fprintf(stderr, "[I::%s] RAM required: %.3fGB\n", __func__, (double) rss_intra / GB);
re = ENOMEM_ERR;
goto scaff_failed_0;
}
rss_limit -= rss_intra;
fprintf(stderr, "[I::%s] starting norm estimation...\n", __func__);
intra_link_mat_t *intra_link_mat = intra_link_mat_from_file(link_file, cov_norm, dict, re_cuts, resolution, 1, mq);
#ifdef DEBUG_RAM_USAGE
fprintf(stderr, "[DEBUG_RAM_USAGE::%s] RAM peak: %.3fGB\n", __func__, (double) peakrss() / GB);
fprintf(stderr, "[DEBUG_RAM_USAGE::%s] RAM intra: %.3fGB\n", __func__, (double) rss_intra / GB);
fprintf(stderr, "[DEBUG_RAM_USAGE::%s] RAM free: %.3fGB\n", __func__, (double) rss_limit / GB);
#endif
norm_t *norm = calc_norms(intra_link_mat, d_min_cell, d_mass_frac);
if (norm == 0) {
fprintf(stderr, "[W::%s] No enough bands for norm calculation... End of scaffolding round.\n", __func__);
re = ENOBND_ERR;
goto scaff_failed_1;
}
rss_inter = no_mem_check? 0 : estimate_inter_link_mat_init_rss(dict, resolution, norm->r);
if ((rss_limit >= 0 && rss_inter > rss_limit) || rss_inter < 0) {
// no enough memory
fprintf(stderr, "[I::%s] No enough memory. Try lower resolutions... End of scaffolding round.\n", __func__);
fprintf(stderr, "[I::%s] RAM limit: %.3fGB\n", __func__, (double) rss_limit / GB);
fprintf(stderr, "[I::%s] RAM required: %.3fGB\n", __func__, (double) rss_inter / GB);
re = ENOMEM_ERR;
goto scaff_failed_1;
}
rss_limit -= rss_inter;
fprintf(stderr, "[I::%s] starting link estimation...\n", __func__);
inter_link_mat_t *inter_link_mat = inter_link_mat_from_file(link_file, cov_norm, dict, re_cuts, resolution, norm->r, mq);
#ifdef DEBUG_RAM_USAGE
fprintf(stderr, "[DEBUG_RAM_USAGE::%s] RAM peak: %.3fGB\n", __func__, (double) peakrss() / GB);
fprintf(stderr, "[DEBUG_RAM_USAGE::%s] RAM inter: %.3fGB\n", __func__, (double) rss_inter / GB);
fprintf(stderr, "[DEBUG_RAM_USAGE::%s] RAM free: %.3fGB\n", __func__, (double) rss_limit / GB);
#endif
*noise = inter_link_mat->noise / resolution / resolution;
double la;
re = inter_link_norms(inter_link_mat, norm, 1, max_noise_ratio, &la);
if (re) {
goto scaff_failed_2;
}
int8_t *directs = 0;
// directs = calc_link_directs_from_file(link_file, dict);
calc_link_directs(inter_link_mat, .1, dict, directs);
if(directs) free(directs);
#ifdef DEBUG_LINK
fprintf(stderr, "[DEBUG_LINK::%s] print_inter_link_norms\n", __func__);
print_inter_link_norms(stderr, inter_link_mat, dict);
#endif
int8_t *telos;
telos = find_aseq_telos(dict, telo_ends);
fprintf(stderr, "[I::%s] starting scaffolding graph contruction...\n", __func__);
graph_t *g = build_graph_from_links(inter_link_mat, dict, .1, la, telos);
free(telos);
#ifdef DEBUG_GRAPH_PRUNE
fprintf(stderr, "[DEBUG_GRAPH_PRUNE::%s] scaffolding graph (before pruning) in GV format\n", __func__);
graph_print_gv(g, stderr);
fprintf(stderr, "[DEBUG_GRAPH_PRUNE::%s] scaffolding graph (before pruning) in GFA format\n", __func__);
graph_print(g, stderr, 1);
#endif
uint64_t n_arc;
n_arc = g->n_arc;
#ifdef DEBUG_GRAPH_PRUNE
fprintf(stderr, "[DEBUG_GRAPH_PRUNE::%s] number edges before trimming: %ld\n", __func__, n_arc);
int round = 0;
#endif
while (1) {
trim_graph_simple_filter(g, .1, .7, .1, 0);
#ifdef DEBUG_GRAPH_PRUNE
fprintf(stderr, "[DEBUG_GRAPH_PRUNE::%s] number edges after simple trimming round %d: %ld\n", __func__, round, g->n_arc);
graph_print_gv(g, stderr);
#endif
trim_graph_tips(g);
trim_graph_blunts(g);
trim_graph_repeats(g);
trim_graph_transitive_edges(g);
trim_graph_pop_bubbles(g);
trim_graph_pop_undirected(g);
trim_graph_weak_edges(g);
trim_graph_self_loops(g);
#ifdef DEBUG_GRAPH_PRUNE
fprintf(stderr, "[DEBUG_GRAPH_PRUNE::%s] number edges after trimming round %d: %ld\n", __func__, ++round, g->n_arc);
graph_print_gv(g, stderr);
#endif
if (g->n_arc == n_arc)
break;
else
n_arc = g->n_arc;
}
trim_graph_ambiguous_edges(g);
#ifdef DEBUG_GRAPH_PRUNE
fprintf(stderr, "[DEBUG_GRAPH_PRUNE::%s] scaffolding graph (after pruning) in GV format\n", __func__);
graph_print_gv(g, stderr);
fprintf(stderr, "[DEBUG_GRAPH_PRUNE::%s] scaffolding graph (after pruning) in GFA format\n", __func__);
graph_print(g, stderr, 1);
#endif
asm_dict_t *d = make_asm_dict_from_graph(g, g->sdict);
// write scaffolds to AGP file
FILE *agp_out = NULL;
if (out) {
char *agp_out_name = (char *) malloc(strlen(out) + 5);
sprintf(agp_out_name, "%s.agp", out);
agp_out = fopen(agp_out_name, "w");
free(agp_out_name);
} else {
agp_out = fopen("scaffolds_FINAL.agp", "w");
}
if (agp_out == NULL) {
fprintf(stderr, "[E::%s] fail to open file to write\n", __func__);
re = 1;
} else {
write_asm_dict_to_agp(d, agp_out);
fclose(agp_out);
}
asm_destroy(d);
graph_destroy(g);
scaff_failed_2:
inter_link_mat_destroy(inter_link_mat);
scaff_failed_1:
norm_destroy(norm);
intra_link_mat_destroy(intra_link_mat);
scaff_failed_0:
asm_destroy(dict);
sd_destroy(sdict);
return re;
}
int contig_error_break(char *agp, char *fai, char *link_file, uint32_t ml, char *out)
{
uint32_t i, ec_round, err_no, bp_n;
sdict_t *sdict;
asm_dict_t *dict;
int dist_thres;
sdict = make_sdict_from_index(fai, ml);
dict = agp? make_asm_dict_from_agp(sdict, agp, 1) : make_asm_dict_from_sdict(sdict);
dist_thres = estimate_dist_thres_from_file(link_file, dict, ec_min_frac, ec_resolution, 0);
dist_thres = MAX(dist_thres, ec_min_window);
fprintf(stderr, "[I::%s] dist threshold for contig error break: %d\n", __func__, dist_thres);
char* out1 = (char *) malloc(strlen(out) + 35);
ec_round = err_no = 0;
while (1) {
if (ec_round) dict = make_asm_dict_from_agp(sdict, out1, 1);
link_mat_t *link_mat = link_mat_from_file(link_file, dict, dist_thres, ec_bin, .0, ec_move_avg, 0);
#ifdef DEBUG_ERROR_BREAK
fprintf(stderr, "[DEBUG_ERROR_BREAK::%s] ec_round %u link matrix\n", __func__, ec_round);
print_link_mat(link_mat, dict, stderr);
#endif
bp_n = 0;
bp_t *breaks = detect_break_points(link_mat, ec_bin, ec_merge_thresh, ec_fold_thresh, ec_dual_break_thresh, &bp_n);
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] number contig breaks in round %u: %u\n", __func__, ec_round + 1, bp_n);
#endif
sprintf(out1, "%s_%02d.agp", out, ++ec_round);
FILE *agp_out = fopen(out1, "w");
write_break_agp(dict, breaks, bp_n, agp_out);
fclose(agp_out);
link_mat_destroy(link_mat);
asm_destroy(dict);
for (i = 0; i < bp_n; ++i)
free(breaks[i].p);
free(breaks);
err_no += bp_n;
#ifdef DEBUG_ERROR_BREAK
fprintf(stderr, "[DEBUG_ERROR_BREAK::%s] bp_n %d\n", __func__, bp_n);
#endif
if (!bp_n)
break;
}
sd_destroy(sdict);
free(out1);
fprintf(stderr, "[I::%s] performed %u round assembly error correction. Made %u breaks \n", __func__, ec_round, err_no);
return ec_round;
}
int scaffold_error_break(char *fai, char *link_file, uint32_t ml, uint8_t mq, char *agp, int flank_size, double noise, char *out)
{
int dist_thres;
sdict_t *sdict = make_sdict_from_index(fai, ml);
asm_dict_t *dict = make_asm_dict_from_agp(sdict, agp, 1);
dist_thres = flank_size * 2;
//dist_thres = estimate_dist_thres_from_file(link_file, dict, ec_min_frac, ec_resolution);
//dist_thres = MAX(dist_thres, ec_min_window);
//fprintf(stderr, "[I::%s] dist threshold for scaffold error break: %d\n", __func__, dist_thres);
link_mat_t *link_mat = link_mat_from_file(link_file, dict, dist_thres, ec_bin, noise, ec_move_avg, mq);
#ifdef DEBUG_ERROR_BREAK
fprintf(stderr, "[DEBUG_ERROR_BREAK::%s] link matrix\n", __func__);
print_link_mat(link_mat, dict, stderr);
#endif
uint32_t bp_n = 0;
bp_t *breaks = detect_break_points_local_joint(link_mat, ec_bin, ec_fold_thresh, flank_size, dict, &bp_n);
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] number scaffold breaks: %u\n", __func__, bp_n);
#endif
FILE *agp_out = fopen(out, "w");
write_break_agp(dict, breaks, bp_n, agp_out);
fclose(agp_out);
link_mat_destroy(link_mat);
asm_destroy(dict);
sd_destroy(sdict);
int i;
for (i = 0; i < bp_n; ++i)
free(breaks[i].p);
free(breaks);
return bp_n;
}
static void print_asm_stats(uint64_t *n_stats, uint32_t *l_stats, int all)
{
#ifdef DEBUG
int i;
fprintf(stderr, "[I::%s] assembly stats:\n", __func__);
for (i = 0; i < 10; ++i)
fprintf(stderr, "[I::%s] N%d: %lu (n = %u)\n", __func__, (i + 1) * 10, n_stats[i], l_stats[i]);
#else
fprintf(stderr, "[I::%s] assembly stats:\n", __func__);
fprintf(stderr, "[I::%s] N%d: %lu (n = %u)\n", __func__, 50, n_stats[4], l_stats[4]);
fprintf(stderr, "[I::%s] N%d: %lu (n = %u)\n", __func__, 90, n_stats[8], l_stats[8]);
if (all)
fprintf(stderr, "[I::%s] N%d: %lu (n = %u)\n", __func__, 100, n_stats[9], l_stats[9]);
#endif
}
int run_yahs(char *fai, char *agp, char *link_file, uint32_t ml, uint8_t mq, char *out, int *resolutions, int nr, int rr, re_cuts_t *re_cuts, int8_t *telo_ends, uint32_t d_min_cell, double d_mass_frac, int no_contig_ec, int no_scaffold_ec, int no_mem_check)
{
int ec_round, resolution, re, r, rn, rc, ex;
uint64_t n50;
char *out_fn, *out_agp, *out_agp_break;
double noise;
FILE *fo;
sdict_t *sdict;
asm_dict_t *dict;
cov_norm_t *cov_norm;
long rss_total, rss_limit;
ram_limit(&rss_total, &rss_limit);
fprintf(stderr, "[I::%s] RAM total: %.3fGB\n", __func__, (double) rss_total / GB);
fprintf(stderr, "[I::%s] RAM limit: %.3fGB\n", __func__, (double) rss_limit / GB);
if (no_mem_check)
fprintf(stderr, "[I::%s] RAM check disabled\n", __func__);
sdict = make_sdict_from_index(fai, ml);
out_fn = (char *) malloc(strlen(out) + 35);
out_agp = (char *) malloc(strlen(out) + 35);
out_agp_break = (char *) malloc(strlen(out) + 35);
if (no_contig_ec == 0) {
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] perform contig error break...\n", __func__);
#endif
sprintf(out_agp_break, "%s_inital_break", out);
ec_round = contig_error_break(agp, fai, link_file, ml, out_agp_break);
sprintf(out_agp_break, "%s_inital_break_%02d.agp", out, ec_round);
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] contig error break done\n", __func__);
#endif
} else {
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] no contig error break...\n", __func__);
#endif
if (agp != 0) {
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] use input AGP file\n", __func__);
#endif
if (strlen(agp) > strlen(out)) {
free(out_agp_break);
out_agp_break = (char *) malloc(strlen(agp) + 35);
}
sprintf(out_agp_break, "%s", agp);
} else {
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] make AGP file from input FASTA file\n", __func__);
#endif
sprintf(out_agp_break, "%s_no_break.agp", out);
fo = fopen(out_agp_break, "w");
if (fo == NULL) {
fprintf(stderr, "[E::%s] cannot open file %s for writing\n", __func__, out_agp_break);
exit(EXIT_FAILURE);
}
write_sdict_to_agp(sdict, fo);
fclose(fo);
}
}
dict = make_asm_dict_from_agp(sdict, out_agp_break, 1);
if (dict->n > MAX_N_SEQ) {
fprintf(stderr, "[E::%s] sequence number exceeds limit (%d > %d)\n", __func__, dict->n, MAX_N_SEQ);
fprintf(stderr, "[E::%s] consider removing short sequences before scaffolding, or\n", __func__);
fprintf(stderr, "[E::%s] running without error correction (--no-contig-ec) if due to excessive contig error breaks\n", __func__);
fprintf(stderr, "[E::%s] program halted...\n", __func__);
return 1;
}
asm_sd_stats(dict, n_stats, l_stats);
print_asm_stats(n_stats, l_stats, 1);
asm_destroy(dict);
cov_norm = cov_norm_from_file(link_file, sdict);
r = rc = 0;
rn = rr;
ex = max_extra_try;
while (r < nr) {
resolution = resolutions[r];
// dict = make_asm_dict_from_agp(sdict, out_agp_break, 1);
if (n_stats[4] < resolution * 10) {
if (!ex) {
fprintf(stderr, "[I::%s] assembly N50 (%lu) too small. End of scaffolding.\n", __func__, n_stats[4]);
fprintf(stderr, "[I::%s] consider running with increased memory limit if there was a memory issue.\n", __func__);
break;
} else {
if (r > 0)
resolution = resolutions[r - 1]; // use the previous resolution level
else {
resolution /= 10;
if (resolution < 1000)
resolution = 1000;
if (resolution > resolutions[0])
resolution = resolutions[0] / 2;
}
fprintf(stderr, "[I::%s] assembly N50 (%lu) too small.\n", __func__, n_stats[4]);
fprintf(stderr, "[I::%s] do an extra round scaffolding with resolution = %d\n", __func__, resolution);
ex--; // increase extra try number
}
} else {
rn--;
if (!rn || n_stats[8] > resolution * 10) {
r++; // move to the next resolution level
rn = rr;
}
ex = max_extra_try; // reset extra try number
}
rc++;
fprintf(stderr, "[I::%s] scaffolding round %d resolution = %d\n", __func__, rc, resolution);
sprintf(out_fn, "%s_r%02d", out, rc);
// noise per unit
re = run_scaffolding(fai, out_agp_break, link_file, cov_norm, ml, mq, re_cuts, telo_ends, out_fn, resolution,
&noise, d_min_cell, d_mass_frac, rss_limit, no_mem_check);
if (!re) {
sprintf(out_agp, "%s_r%02d.agp", out, rc);
if (no_scaffold_ec == 0) {
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] perform scaffold error break\n", __func__);
#endif
sprintf(out_agp_break, "%s_r%02d_break.agp", out, rc);
scaffold_error_break(fai, link_file, ml, mq, out_agp, resolution, noise, out_agp_break);
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] scaffold error break done\n", __func__);
#endif
} else {
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] no scaffold error break\n", __func__);
#endif
sprintf(out_agp_break, "%s", out_agp);
}
}
// asm_destroy(dict);
fprintf(stderr, "[I::%s] scaffolding round %d done\n", __func__, rc);
dict = make_asm_dict_from_agp(sdict, out_agp_break, 1);
n50 = n_stats[4]; // old n50
asm_sd_stats(dict, n_stats, l_stats);
// no improvements in a retry round
if (ex < max_extra_try && n50 == n_stats[4])
ex = 0;
print_asm_stats(n_stats, l_stats, 0);
asm_destroy(dict);
/***
if (re && re != ENOMEM_ERR) {
fprintf(stderr, "[I::%s] Reach data limit for HiC contact density estimation in lower resulutions. End of scaffolding.\n", __func__);
break;
}
**/
}
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] make final output...\n", __func__);
#endif
sprintf(out_agp, "%s_scaffolds_final.agp", out);
// output sorted agp by scaffold size instead of file copy
// file_copy(out_agp_break, out_agp);
if (ml > 0) {
// add short sequences to dict
#ifdef DEBUG
fprintf(stderr, "[DEBUG::%s] add unused short sequences back...\n", __func__);
#endif
sd_destroy(sdict);
sdict = make_sdict_from_index(fai, 0);
dict = make_asm_dict_from_agp(sdict, out_agp_break, 1);
add_unplaced_short_seqs(dict, ml);
} else {
dict = make_asm_dict_from_agp(sdict, out_agp_break, 1);
}
fo = fopen(out_agp, "w");
if (fo == NULL) {
fprintf(stderr, "[E::%s] cannot open file %s for writing\n", __func__, out_agp);
exit(EXIT_FAILURE);
}
write_sorted_agp(dict, fo);
fclose(fo);
asm_destroy(dict);
sd_destroy(sdict);
cov_norm_destroy(cov_norm);
free(out_agp);
free(out_fn);
free(out_agp_break);
return 0;
}
#ifndef DEBUG_GT4G
static int default_resolutions[15] = {10000, 20000, 50000, 100000, 200000, 500000, 1000000, 2000000, 5000000, 10000000, 20000000, 50000000, 100000000, 200000000, 500000000};
#else
static int default_resolutions[13] = {50000, 100000, 250000, 500000, 1000000, 2500000, 5000000, 10000000, 25000000, 50000000, 100000000, 250000000, 500000000};
#endif
static int default_nr(char *fai, uint32_t ml)
{
int i, max_res, nr;
int64_t genome_size;
genome_size = 0;
sdict_t *sdict = make_sdict_from_index(fai, ml);
for (i = 0; i < sdict->n; ++i)
genome_size += sdict->s[i].len;
sd_destroy(sdict);
max_res = 0;
if (genome_size < 100000000)
max_res = 1000000;
else if (genome_size < 200000000)
max_res = 2000000;
else if (genome_size < 500000000)
max_res = 5000000;
else if (genome_size < 1000000000)
max_res = 10000000;
else if (genome_size < 2000000000)
max_res = 20000000;
else if (genome_size < 5000000000)
max_res = 50000000;
else if (genome_size < 10000000000)
max_res = 100000000;
else if (genome_size < 20000000000)
max_res = 200000000;
else
max_res = 500000000;
nr = 0;
while (nr < sizeof(default_resolutions) / sizeof(int) && default_resolutions[nr] <= max_res)
++nr;
return nr;
}
static void print_help(FILE *fp_help, int is_long_help)
{
fprintf(fp_help, "Usage: yahs [options] <contigs.fa> <hic.bed>|<hic.bam>|<hic.pa5>|<hic.bin>\n");
fprintf(fp_help, "Options:\n");
fprintf(fp_help, " -a FILE AGP file (for rescaffolding) [none]\n");
fprintf(fp_help, " -r INT[,INT,...] list of resolutions in ascending order [automate]\n");
fprintf(fp_help, " -R INT rounds to run at each resoultion level [1]\n");
fprintf(fp_help, " -e STR restriction enzyme cutting sites [none]\n");
fprintf(fp_help, " -l INT minimum length of a contig to scaffold [0]\n");
fprintf(fp_help, " -q INT minimum mapping quality [10]\n");
fprintf(fp_help, "\n");
fprintf(fp_help, " --no-contig-ec do not do contig error correction\n");
fprintf(fp_help, " --no-scaffold-ec do not do scaffold error correction\n");
fprintf(fp_help, " --no-mem-check do not do memory check at runtime\n");
fprintf(fp_help, " --file-type STR input file type BED|BAM|PA5|BIN, file name extension is ignored if set\n");
fprintf(fp_help, " --read-length read length (required for PA5 format input) [150]\n");
fprintf(fp_help, " --telo-motif STR telomeric sequence motif\n");
if (is_long_help) {
fprintf(fp_help, "\n");
fprintf(fp_help, " --D-min-cells INT minimum number of cells to calculate the distance threshold [30]\n");
fprintf(fp_help, " --D-mass-frac FLOAT fraction of HiC signals to calculate the distance threshold [0.99]\n");
fprintf(fp_help, "\n");
fprintf(fp_help, " --seq-ctype STR AGP output sequence component type [%s]\n", agp_component_type_val(DEFAULT_AGP_SEQ_COMPONENT_TYPE));
fprintf(fp_help, " --gap-ctype STR AGP output gap component type [%s]\n", agp_component_type_val(DEFAULT_AGP_GAP_COMPONENT_TYPE));
fprintf(fp_help, " --gap-link STR AGP output gap linkage evidence [%s]\n", agp_linkage_evidence_val(DEFAULT_AGP_LINKAGE_EVIDENCE));
fprintf(fp_help, " --gap-size INT AGP output gap size between sequence component [%d]\n", DEFAULT_AGP_GAP_SIZE);
fprintf(fp_help, "\n");
fprintf(fp_help, " --convert-to-binary make a binary ouput file from the input and exit\n");
fprintf(fp_help, " --print-telo-motifs print telomeric motifs in the database and exit\n");
fprintf(fp_help, " --search-telo-ends search telomeric ends in the sequences and exit\n");
}
fprintf(fp_help, "\n");
fprintf(fp_help, " -o STR prefix of output files [yahs.out]\n");
fprintf(fp_help, " -v INT verbose level [%d]\n", VERBOSE);
fprintf(fp_help, " -? print long help with extra option list\n");
fprintf(fp_help, " --version show version number\n");
}
static ko_longopt_t long_options[] = {
{ "no-contig-ec", ko_no_argument, 301 },
{ "no-scaffold-ec", ko_no_argument, 302 },
{ "no-mem-check", ko_no_argument, 303 },
{ "D-min-cells", ko_required_argument, 304 },
{ "D-mass-frac", ko_required_argument, 305 },
{ "file-type", ko_required_argument, 306 },
{ "seq-ctype", ko_required_argument, 307 },
{ "gap-ctype", ko_required_argument, 308 },
{ "gap-link", ko_required_argument, 309 },
{ "gap-size", ko_required_argument, 310 },
{ "read-length", ko_required_argument, 311 },
{ "telo-motif", ko_required_argument, 312 },
{ "print-telo-motifs", ko_no_argument, 313 },
{ "search-telo-ends", ko_no_argument, 314 },
{ "convert-to-binary", ko_no_argument, 315 },
{ "help", ko_no_argument, 'h' },
{ "version", ko_no_argument, 'V' },
{ 0, 0, 0 }
};
typedef struct {size_t n, m; char **a;} cstr_v;
int main(int argc, char *argv[])
{
if (argc < 2) {
print_help(stderr, 0);
return 1;
}
liftrlimit();
ys_realtime0 = realtime();
char *fa, *fai, *agp, *link_file, *out, *restr, *ecstr, *ext1, *ext2, *link_bin_file, *agp_final, *fa_final;
int *resolutions, nr, rr, mq, ml, rl;
int no_contig_ec, no_scaffold_ec, no_mem_check, d_min_cell, print_telomotifs, search_teloends, convert_binary;
int8_t *telo_ends;
double q_drop, d_mass_frac;
re_cuts_t *re_cuts;
enum fileTypes f_type;
const char *opt_str = "a:e:r:R:o:l:q:Vv:h";
ketopt_t opt = KETOPT_INIT;
int c, ret, is_long_help;
FILE *fp_help = stderr;
ret = 0;
fa = fai = agp = link_file = out = restr = link_bin_file = agp_final = fa_final = 0;
no_contig_ec = no_scaffold_ec = no_mem_check = 0;
resolutions = 0;
telo_ends = 0;
re_cuts = 0;
rr = 1;
mq = 10;
ml = 0;
rl = 150;
ecstr = 0;
q_drop = 0.1;
d_min_cell = 30;
d_mass_frac = 0.99;
convert_binary = 0;
print_telomotifs = 0;
search_teloends = 0;
f_type = NOSET;
is_long_help = 0;
while ((c = ketopt(&opt, argc, argv, 1, opt_str, long_options)) >= 0) {
if (c == 'a') {
agp = opt.arg;
} else if (c == 'r') {
restr = opt.arg;
} else if (c == 'R') {
rr = atoi(opt.arg);
} else if (c == 'o') {
out = opt.arg;
} else if (c == 'l') {
ml = atoi(opt.arg);
} else if (c == 'q') {
mq = atoi(opt.arg);
} else if (c == 'e') {
// make a copy of ecstr to make sure the CMD correct
ecstr = strdup(opt.arg);
} else if (c == 301) {
no_contig_ec = 1;
} else if (c == 302) {
no_scaffold_ec = 1;
} else if (c == 303) {
no_mem_check = 1;
} else if (c == 304) {
d_min_cell = atoi(opt.arg);
} else if (c == 305) {
d_mass_frac = atof(opt.arg);
} else if (c == 306) {
if (strcasecmp(opt.arg, "BED") == 0)
f_type = BED;
else if (strcasecmp(opt.arg, "BAM") == 0)
f_type = BAM;
else if (strcasecmp(opt.arg, "BIN") == 0)
f_type = BIN;
else if (strcasecmp(opt.arg, "PA5") == 0)
f_type = PA5;
else {
fprintf(stderr, "[E::%s] unknown file type: \"%s\"\n", __func__, opt.arg);
return 1;
}
} else if (c == 307) {
DEFAULT_AGP_SEQ_COMPONENT_TYPE = agp_component_type_key(opt.arg);
if (DEFAULT_AGP_SEQ_COMPONENT_TYPE == AGP_CT_N ||
DEFAULT_AGP_SEQ_COMPONENT_TYPE == AGP_CT_U)
fprintf(stderr, "[W::%s] a GAP component identifier will be used for sequences: %s\n",
__func__, opt.arg);
} else if (c == 308) {
DEFAULT_AGP_GAP_COMPONENT_TYPE = agp_component_type_key(opt.arg);
if (DEFAULT_AGP_GAP_COMPONENT_TYPE != AGP_CT_N &&
DEFAULT_AGP_GAP_COMPONENT_TYPE != AGP_CT_U)
fprintf(stderr, "[W::%s] a SEQ component identifier will be used for gaps: %s\n",
__func__, opt.arg);
} else if (c == 309) {
DEFAULT_AGP_LINKAGE_EVIDENCE = agp_linkage_evidence_key(opt.arg);
} else if (c == 310) {
DEFAULT_AGP_GAP_SIZE = atoi(opt.arg);
} else if (c == 311) {
rl = atoi(opt.arg);
} else if (c == 312) {
telo_motif = opt.arg;
} else if (c == 313) {
print_telomotifs = 1;
} else if (c == 314) {
search_teloends = 1;
} else if (c == 315) {
convert_binary = 1;
} else if (c == 'v') {
VERBOSE = atoi(opt.arg);
} else if (c == 'V') {
puts(YAHS_VERSION);
return 0;
} else if (c == 'h') {
fp_help = stdout;
} else if (c == '?') {
if (argv[opt.i - 1][1] == '?') {
fp_help = stdout;
is_long_help = 1;
} else {
fprintf(stderr, "[E::%s] unknown option: \"%s\"\n", __func__, argv[opt.i - 1]);
return 1;
}
} else if (c == ':') {
fprintf(stderr, "[E::%s] missing option: \"%s\"\n", __func__, argv[opt.i - 1]);
return 1;
}
}
if (fp_help == stdout) {
print_help(stdout, is_long_help);
return 0;
}
if (print_telomotifs) {
fprintf(stderr, "[I::%s] telomeric motifs in the database:\n", __func__);
list_telo_motifs(stderr);
return 0;
}
if (search_teloends) {
if (argc - opt.ind < 1) {
fprintf(stderr, "[E::%s] missing input: need a FASTA file\n", __func__);
return 1;
}
if (out != 0 && strcmp(out, "-") != 0) {
if (freopen(out, "wb", stdout) == NULL) {
fprintf(stderr, "[ERROR]\033[1;31m failed to write the output to file '%s'\033[0m: %s\n", out, strerror(errno));
return 1;
}
}
fprintf(stderr, "[I::%s] search telomeric ends in the sequence\n", __func__);
telo_ends = telo_finder(argv[opt.ind], 0, stdout);
if (fflush(stdout) == EOF) {
fprintf(stderr, "[E::%s] failed to write the results\n", __func__);
return 1;
}
if (telo_ends)
free(telo_ends);
goto print_command;
}
if (argc - opt.ind < 2) {
fprintf(stderr, "[E::%s] missing input: two positional options required\n", __func__);
print_help(stderr, is_long_help);
return 1;
}
if (mq < 0 || mq > 255) {
fprintf(stderr, "[E::%s] invalid mapping quality threshold: %d\n", __func__, mq);
return 1;
}
if (ml < 0) {
fprintf(stderr, "[E::%s] invalid contig length threshold: %d\n", __func__, ml);
return 1;
}
if (rl < 0) {
fprintf(stderr, "[E::%s] invalid read length: %d\n", __func__, rl);
return 1;
}
if (check_motif(telo_motif)) {
fprintf(stderr, "[E::%s] invalid telomeric motif string: %s\n", __func__, telo_motif);
return 1;
}
if (rr < 1) {
rr = 1;
fprintf(stderr, "[W::%s] set round number to %d\n", __func__, rr);
}
if (d_min_cell < 10) {
d_min_cell = 10;
fprintf(stderr, "[W::%s] using cell threshold for D: %d\n", __func__, d_min_cell);
}
if (d_mass_frac < 0.8) {
d_mass_frac = 0.8;
fprintf(stderr, "[W::%s] using mass fraction threshold for D: %.2f\n", __func__, d_mass_frac);
}
if (d_mass_frac > 1.0) {
d_mass_frac = 1.0;
fprintf(stderr, "[W::%s] using mass fraction threshold for D: %.2f\n", __func__, d_mass_frac);
}
if (DEFAULT_AGP_GAP_COMPONENT_TYPE == AGP_CT_U && DEFAULT_AGP_GAP_SIZE != DEFAULT_AGP_U_GAP_SIZE)
fprintf(stderr, "[W::%s] type 'U' gap size is not %d\n", __func__, DEFAULT_AGP_U_GAP_SIZE);
fa = argv[opt.ind];
link_file = argv[opt.ind + 1];
if (f_type == NOSET) {
ext1 = strlen(link_file) >= 4? (link_file + strlen(link_file) - 4) : NULL;
ext2 = strlen(link_file) >= 7? (link_file + strlen(link_file) - 7) : NULL;
if (ext1 && !strcasecmp(ext1, ".bam")) f_type = BAM;
else if (ext1 && !strcasecmp(ext1, ".bin")) f_type = BIN;
else if ((ext1 && !strcasecmp(ext1, ".bed")) || (ext2 && !strcasecmp(ext2, ".bed.gz"))) f_type = BED;
else if ((ext1 && !strcasecmp(ext1, ".pa5")) || (ext2 && !strcasecmp(ext2, ".pa5.gz"))) f_type = PA5;
else {
fprintf(stderr, "[E::%s] unknown link file format. File extension .bam, .bed, .pa5 or .bin or --file-type is expected\n", __func__);
exit(EXIT_FAILURE);
}
}
if (f_type == BIN && (strcmp(link_file, "-") == 0 || *link_file == '<')) {
fprintf(stderr, "[E::%s] BIN file format from STDIN is not supported\n", __func__);
exit(EXIT_FAILURE);
}
uint8_t mq8;
mq8 = (uint8_t) mq;
if (out == 0)
out = "yahs.out";
fai = (char *) malloc(strlen(fa) + 5);
sprintf(fai, "%s.fai", fa);
if (restr) {
// resolutions
int max_n_res = 128;
char *eptr, *fptr;
resolutions = (int *) malloc(max_n_res * sizeof(int));
nr = 0;
resolutions[nr++] = strtol(restr, &eptr, 10);