forked from samtools/samtools
-
Notifications
You must be signed in to change notification settings - Fork 0
/
bam_ampliconclip.c
1079 lines (881 loc) · 33.4 KB
/
bam_ampliconclip.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
/* bam_ampliconclip.c -- loads amplicon primers from a BED file and cuts reads
from the 5' end.
Copyright (C) 2020-2021 Genome Research Ltd.
Authors: Andrew Whitwham <[email protected]>
Rob Davies <[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
*/
#include <config.h>
#include <assert.h>
#include <stdbool.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <errno.h>
#include "htslib/thread_pool.h"
#include "sam_opts.h"
#include <htslib/hts.h>
#include "htslib/hfile.h"
#include "htslib/kstring.h"
#include "htslib/sam.h"
#include "samtools.h"
#include "bam_ampliconclip.h"
typedef enum {
soft_clip,
hard_clip
} clipping_type;
typedef struct {
int add_pg;
int use_strand;
int write_clipped;
int mark_fail;
int both;
int fail_len;
int filter_len;
int unmapped;
int oa_tag;
int del_tag;
int tol;
char *arg_list;
char *stats_file;
char *rejects_file;
} cl_param_t;
static int bed_entry_sort(const void *av, const void *bv) {
bed_entry_t *a = (bed_entry_t *) av;
bed_entry_t *b = (bed_entry_t *) bv;
return a->right < b->right ? -1 : (a->right == b->right ? 0 : 1);
}
int load_bed_file_multi_ref(char *infile, int get_strand, int sort_by_pos, khash_t(bed_list_hash) *bed_lists) {
hFILE *fp;
int line_count = 0, ret;
int64_t left, right;
kstring_t line = KS_INITIALIZE;
bed_entry_list_t *list;
khiter_t bed_itr;
if ((fp = hopen(infile, "r")) == NULL) {
print_error_errno("amplicon", "unable to open file %s.", infile);
return 1;
}
char ref[1024];
while (line.l = 0, kgetline(&line, (kgets_func *)hgets, fp) >= 0) {
line_count++;
int hret;
char strand;
if (line.l == 0 || *line.s == '#') continue;
if (strncmp(line.s, "track ", 6) == 0) continue;
if (strncmp(line.s, "browser ", 8) == 0) continue;
if (get_strand) {
if (sscanf(line.s, "%1023s %"SCNd64" %"SCNd64" %*s %*s %c",
ref, &left, &right, &strand) != 4) {
fprintf(stderr, "[amplicon] error: bad bed file format in line %d of %s.\n"
"(N.B. ref/chrom name limited to 1023 characters.)\n",
line_count, infile);
ret = 1;
goto error;
}
} else {
if (sscanf(line.s, "%1023s %"SCNd64" %"SCNd64,
ref, &left, &right) != 3) {
fprintf(stderr, "[amplicon] error: bad bed file format in line %d of %s\n"
"(N.B. ref/chrom name limited to 1023 characters.)\n",
line_count, infile);
ret = 1;
goto error;
}
}
bed_itr = kh_get(bed_list_hash, bed_lists, ref);
if (bed_itr == kh_end(bed_lists)) { // new ref entry
char *ref_name = strdup(ref); // need a copy for the hash key
if (!ref_name) {
fprintf(stderr, "[amplicon] error: unable to allocate memory for ref name.\n");
ret = 1;
goto error;
}
bed_itr = kh_put(bed_list_hash, bed_lists, ref_name, &hret);
if (hret > 0) {
list = &kh_val(bed_lists, bed_itr);
// initialise the new hash entry
list->longest = 0;
list->size = 0;
list->length = 0;
list->bp = NULL;
} else {
fprintf(stderr, "[amplicon] error: ref hashing failure.\n");
ret = 1;
goto error;
}
} else { // existing ref
list = &kh_val(bed_lists, bed_itr);
}
if (list->length == list->size) {
bed_entry_t *tmp;
list->size += list->size / 2 + 256;
if ((tmp = realloc(list->bp, list->size * sizeof(bed_entry_t))) == NULL) {
fprintf(stderr, "[amplicon] error: unable to allocate more memory for bed data.\n");
ret = 1;
goto error;
}
list->bp = tmp;
}
list->bp[list->length].left = left;
list->bp[list->length].right = right;
if (get_strand) {
if (strand == '+') {
list->bp[list->length].rev = 0;
} else if (strand == '-') {
list->bp[list->length].rev = 1;
} else {
fprintf(stderr, "[amplicon] error: bad strand value in line %d, expecting '+' or '-', found '%c'.\n",
line_count, strand);
ret = 1;
goto error;
}
}
if (right - left > list->longest)
list->longest = right - left;
list->length++;
}
if (sort_by_pos) {
for (bed_itr = kh_begin(bed_lists); bed_itr != kh_end(bed_lists); ++bed_itr) {
if (kh_exist(bed_lists, bed_itr)) {
list = &kh_val(bed_lists, bed_itr);
qsort(list->bp, list->length, sizeof(list->bp[0]), bed_entry_sort);
}
}
}
if (kh_size(bed_lists) > 0) {// any entries
ret = 0;
} else {
ret = 1;
}
error:
ks_free(&line);
if (hclose(fp) != 0) {
fprintf(stderr, "[amplicon] warning: failed to close %s", infile);
}
return ret;
}
void destroy_bed_hash(khash_t(bed_list_hash) *hash) {
khiter_t itr;
for (itr = kh_begin(hash); itr != kh_end(hash); ++itr) {
if (kh_exist(hash, itr)) {
free(kh_val(hash, itr).bp);
free((char *)kh_key(hash, itr));
kh_key(hash, itr) = NULL;
}
}
kh_destroy(bed_list_hash, hash);
}
static int matching_clip_site(bed_entry_list_t *sites, hts_pos_t pos,
int is_rev, int use_strand, int64_t longest,
cl_param_t *param) {
int i, size; // may need this to be variable
int tol = param->tol;
int l = 0, mid = sites->length / 2, r = sites->length;
int pos_tol = is_rev ? (pos > tol ? pos - tol : 0) : pos;
while (r - l > 1) {
if (sites->bp[mid].right <= pos_tol) {
l = mid;
} else {
r = mid;
}
mid = (l + r) / 2;
}
size = 0;
for (i = l; i < sites->length; i++) {
hts_pos_t mod_left, mod_right;
if (use_strand && is_rev != sites->bp[i].rev)
continue;
if (is_rev) {
mod_left = sites->bp[i].left;
mod_right = sites->bp[i].right + tol;
} else {
if (sites->bp[i].left > tol) {
mod_left = sites->bp[i].left - tol;
} else {
mod_left = 0;
}
mod_right = sites->bp[i].right;
}
if (pos + longest + tol < mod_right)
break;
if (pos >= mod_left && pos <= mod_right) {
if (is_rev) {
if (size < pos - sites->bp[i].left) {
size = pos - sites->bp[i].left;
}
} else {
if (size < sites->bp[i].right - pos) {
size = sites->bp[i].right - pos;
}
}
}
}
return size;
}
static int bam_trim_left(bam1_t *rec, bam1_t *rec_out, uint32_t bases,
clipping_type clipping) {
uint32_t *orig_cigar = bam_get_cigar(rec);
uint8_t *orig_seq = bam_get_seq(rec);
uint8_t *orig_qual = bam_get_qual(rec);
uint8_t *orig_aux = bam_get_aux(rec);
uint32_t *new_cigar;
uint8_t *new_qual;
size_t orig_l_aux = bam_get_l_aux(rec);
uint32_t i, j, odd_base = 0;
uint32_t ref_remove = bases, qry_removed = 0, hardclip = 0;
hts_pos_t new_pos = rec->core.pos;
uint32_t cig_type, cig_op;
if (rec->l_data + 8 > rec_out->m_data) {
uint8_t *new_data = realloc(rec_out->data, rec->l_data + 8);
if (!new_data) {
fprintf(stderr, "[ampliconclip] error: could not allocate memoy for new bam record\n");
return 1;
}
rec_out->data = new_data;
rec_out->m_data = rec->l_data + 8;
}
// Copy core data & name
memcpy(&rec_out->core, &rec->core, sizeof(rec->core));
memcpy(rec_out->data, rec->data, rec->core.l_qname);
if (clipping == hard_clip && bases >= rec->core.l_qseq) {
rec_out->core.l_qseq = 0;
rec_out->core.n_cigar = 0;
if (orig_l_aux)
memcpy(bam_get_aux(rec_out), orig_aux, orig_l_aux);
rec_out->l_data = bam_get_aux(rec_out) - rec_out->data + orig_l_aux;
return 0;
}
// Modify CIGAR
new_cigar = bam_get_cigar(rec_out);
for (i = 0; i < rec->core.n_cigar; i++) {
cig_op = bam_cigar_op(orig_cigar[i]);
cig_type = bam_cigar_type(cig_op);
if (cig_op == BAM_CHARD_CLIP) {
hardclip += bam_cigar_oplen(orig_cigar[i]);
} else {
if (cig_type & 2) {
if (bam_cigar_oplen(orig_cigar[i]) <= ref_remove) {
ref_remove -= bam_cigar_oplen(orig_cigar[i]);
} else {
break;
}
new_pos += bam_cigar_oplen(orig_cigar[i]);
}
if (cig_type & 1) {
qry_removed += bam_cigar_oplen(orig_cigar[i]);
}
}
}
if (i < rec->core.n_cigar) {
cig_type = bam_cigar_type(bam_cigar_op(orig_cigar[i]));
// account for the last operation
if (cig_type & 2) {
new_pos += ref_remove;
}
if (cig_type & 1) {
qry_removed += ref_remove;
}
} else {
qry_removed = rec->core.l_qseq;
}
j = 0;
if (clipping == hard_clip && hardclip + qry_removed > 0) {
new_cigar[j++] = bam_cigar_gen(hardclip + qry_removed, BAM_CHARD_CLIP);
}
if (clipping == soft_clip) {
if (hardclip > 0) {
new_cigar[j++] = bam_cigar_gen(hardclip, BAM_CHARD_CLIP);
}
if (qry_removed > 0) {
new_cigar[j++] = bam_cigar_gen(qry_removed, BAM_CSOFT_CLIP);
}
}
if (i < rec->core.n_cigar
&& bam_cigar_oplen(orig_cigar[i]) > ref_remove) {
new_cigar[j++] = bam_cigar_gen(bam_cigar_oplen(orig_cigar[i]) - ref_remove, bam_cigar_op(orig_cigar[i]));
// fill in the rest of the cigar
i++;
for (; i < rec->core.n_cigar; i++) {
new_cigar[j++] = orig_cigar[i];
}
}
rec_out->core.n_cigar = j;
if (clipping == soft_clip) {
qry_removed = 0; // Copy all the sequence and confidence values
odd_base = 1; // account for an odd number of bases
}
new_qual = bam_get_seq(rec_out) + (rec->core.l_qseq - qry_removed + 1) / 2;
// Copy remaining SEQ
if ((qry_removed & 1) == 0) {
memcpy(bam_get_seq(rec_out), orig_seq + (qry_removed / 2),
(rec->core.l_qseq - qry_removed + odd_base) / 2);
} else {
uint8_t *in = orig_seq + qry_removed / 2;
uint8_t *out = bam_get_seq(rec_out);
uint32_t i;
for (i = qry_removed; i < rec->core.l_qseq - 1; i += 2) {
*out++ = ((in[0] & 0x0f) << 4) | ((in[1] & 0xf0) >> 4);
in++;
}
if (i < rec->core.l_qseq) {
*out++ = (in[0] & 0x0f) << 4;
}
assert(out == new_qual);
}
// Copy remaining QUAL
memmove(new_qual, orig_qual, rec->core.l_qseq - qry_removed);
// Set new l_qseq
rec_out->core.l_qseq -= qry_removed;
// Move AUX
if (orig_l_aux)
memcpy(bam_get_aux(rec_out), orig_aux, orig_l_aux);
// Set new l_data
rec_out->l_data = bam_get_aux(rec_out) - rec_out->data + orig_l_aux;
// put in new pos
rec_out->core.pos = new_pos;
return 0;
}
static int bam_trim_right(bam1_t *rec, bam1_t *rec_out, uint32_t bases,
clipping_type clipping) {
uint32_t *orig_cigar = bam_get_cigar(rec);
uint8_t *orig_seq = bam_get_seq(rec);
uint8_t *orig_qual = bam_get_qual(rec);
uint8_t *orig_aux = bam_get_aux(rec);
uint32_t *new_cigar;
uint32_t new_n_cigar = 0;
uint8_t *new_qual;
size_t orig_l_aux = bam_get_l_aux(rec);
int32_t i;
int32_t j;
uint32_t ref_remove = bases, qry_removed = 0, hardclip = 0;
uint32_t cig_type, cig_op;
if (rec->l_data + 8 > rec_out->m_data) {
uint8_t *new_data = realloc(rec_out->data, rec->l_data + 8);
if (!new_data) {
fprintf(stderr, "[ampliconclip] error: could not allocate memoy for new bam record\n");
return 1;
}
rec_out->data = new_data;
rec_out->m_data = rec->l_data + 8;
}
// Copy core data & name
memcpy(&rec_out->core, &rec->core, sizeof(rec->core));
memcpy(rec_out->data, rec->data, rec->core.l_qname);
if (clipping == hard_clip && bases >= rec->core.l_qseq) {
rec_out->core.l_qseq = 0;
rec_out->core.n_cigar = 0;
if (orig_l_aux)
memcpy(bam_get_aux(rec_out), orig_aux, orig_l_aux);
rec_out->l_data = bam_get_aux(rec_out) - rec_out->data + orig_l_aux;
return 0;
}
// Modify CIGAR here
new_cigar = bam_get_cigar(rec_out);
for (i = rec->core.n_cigar - 1; i >= 0; --i) {
cig_op = bam_cigar_op(orig_cigar[i]);
cig_type = bam_cigar_type(cig_op);
if (cig_op == BAM_CHARD_CLIP) {
hardclip += bam_cigar_oplen(orig_cigar[i]);
} else {
if (cig_type & 2) {
if (bam_cigar_oplen(orig_cigar[i]) <= ref_remove) {
ref_remove -= bam_cigar_oplen(orig_cigar[i]);
} else {
break;
}
}
if (cig_type & 1) {
qry_removed += bam_cigar_oplen(orig_cigar[i]);
}
}
}
if (i >= 0) {
cig_type = bam_cigar_type(bam_cigar_op(orig_cigar[i]));
if (cig_type & 1) {
qry_removed += ref_remove;
}
j = i;
if (qry_removed > 0) j++;
if (hardclip > 0 && (clipping == soft_clip || qry_removed == 0)) j++;
} else {
qry_removed = rec->core.l_qseq;
j = 0;
if (hardclip > 0 && clipping == soft_clip) j++;
}
if (clipping == hard_clip && hardclip + qry_removed > 0) {
new_cigar[j] = bam_cigar_gen(hardclip + qry_removed, BAM_CHARD_CLIP);
new_n_cigar++;
}
if (clipping == soft_clip) {
if (hardclip > 0) {
new_cigar[j] = bam_cigar_gen(hardclip, BAM_CHARD_CLIP);
new_n_cigar++;
if (qry_removed > 0) --j;
}
if (qry_removed > 0) {
new_cigar[j] = bam_cigar_gen(qry_removed, BAM_CSOFT_CLIP);
new_n_cigar++;
}
}
if (j > 0) {
new_cigar[--j] = bam_cigar_gen(bam_cigar_oplen(orig_cigar[i]) - ref_remove, bam_cigar_op(orig_cigar[i]));
new_n_cigar++;
}
// fill in the rest of the cigar
while (j > 0) {
new_cigar[--j] = orig_cigar[--i];
new_n_cigar++;
}
rec_out->core.n_cigar = new_n_cigar;
if (clipping == soft_clip)
qry_removed = 0; // Copy all the sequence and confidence values
new_qual = bam_get_seq(rec_out) + (rec->core.l_qseq - qry_removed + 1) / 2;
// Copy remaining SEQ
memcpy(bam_get_seq(rec_out), orig_seq, (rec->core.l_qseq - qry_removed + 1) / 2);
// Copy remaining QUAL
memcpy(new_qual, orig_qual, rec->core.l_qseq - qry_removed);
// Set new l_qseq
rec_out->core.l_qseq -= qry_removed;
// Copy AUX
if (orig_l_aux)
memcpy(bam_get_aux(rec_out), orig_aux, orig_l_aux);
// Set new l_data
rec_out->l_data = bam_get_aux(rec_out) - rec_out->data + orig_l_aux;
return 0;
}
static hts_pos_t active_query_len(bam1_t *b) {
uint32_t *cigar = bam_get_cigar(b);
uint32_t cig_type, cig_op;
hts_pos_t len = 0;
int i;
for (i = 0; i < b->core.n_cigar; i++) {
cig_op = bam_cigar_op(cigar[i]);
cig_type = bam_cigar_type(cig_op);
if ((cig_type & 1) && (cig_op != BAM_CSOFT_CLIP)) {
len += bam_cigar_oplen(cigar[i]);
}
}
return len;
}
static inline void swap_bams(bam1_t **a, bam1_t **b) {
bam1_t *tmp = *a;
*a = *b;
*b = tmp;
}
// Format OA:Z:(RNAME,POS,strand,CIGAR,MAPQ,NM;
static inline int tag_original_data(bam1_t *orig, kstring_t *oa_tag) {
char strand;
uint8_t *nm_tag, *old_oa_tag;
uint32_t *cigar;
int64_t nm = 0;
int i, res = 0;
ks_clear(oa_tag);
// if there is an existing OA tag the new one gets appended to it
if ((old_oa_tag = bam_aux_get(orig, "OA"))) {
res |= ksprintf(oa_tag, "%s", bam_aux2Z(old_oa_tag)) < 0;
}
if (orig->core.flag & BAM_FREVERSE)
strand = '-';
else
strand = '+';
if ((nm_tag = bam_aux_get(orig, "NM"))) {
nm = bam_aux2i(nm_tag);
}
res |= ksprintf(oa_tag, "%s,%"PRIhts_pos",%c,", bam_get_qname(orig), orig->core.pos + 1, strand) < 0;
for (i = 0, cigar = bam_get_cigar(orig); i < orig->core.n_cigar && res == 0; ++i) {
res |= kputw(bam_cigar_oplen(cigar[i]), oa_tag) < 0;
res |= kputc(bam_cigar_opchr(cigar[i]), oa_tag) < 0;
}
if (nm_tag) {
res |= ksprintf(oa_tag, ",%d,%"PRId64";", orig->core.qual, nm) < 0;
} else {
res |= ksprintf(oa_tag, "%d,;", orig->core.qual) < 0;
}
return res;
}
static int bam_clip(samFile *in, samFile *out, samFile *reject, char *bedfile,
clipping_type clipping, cl_param_t *param) {
int ret = 1, r, file_open = 0;
bam_hdr_t *header = NULL;
bam1_t *b = NULL, *b_tmp = NULL;
long f_count = 0, r_count = 0, n_count = 0, l_count = 0, l_exclude = 0, b_count = 0;
long filtered = 0, written = 0, failed = 0;
kstring_t str = KS_INITIALIZE;
kstring_t oat = KS_INITIALIZE;
bed_entry_list_t *sites;
FILE *stats_fp = stderr;
khash_t(bed_list_hash) *bed_hash = kh_init(bed_list_hash);
if (load_bed_file_multi_ref(bedfile, param->use_strand, 1, bed_hash)) {
fprintf(stderr, "[ampliconclip] error: unable to load bed file.\n");
goto fail;
}
if ((header = sam_hdr_read(in)) == NULL) {
fprintf(stderr, "[ampliconclip] error: could not read header\n");
goto fail;
}
// changing pos can ruin coordinate sort order
if (sam_hdr_find_tag_hd(header, "SO", &str) == 0 && str.s && strcmp(str.s, "coordinate") == 0) {
const char *new_order = "unknown";
if (sam_hdr_update_hd(header, "SO", new_order) == -1) {
fprintf(stderr, "[ampliconclip] error: unable to change sort order to 'SO:%s'\n", new_order);
goto fail;
}
}
ks_free(&str);
if (param->add_pg && sam_hdr_add_pg(header, "samtools", "VN", samtools_version(),
param->arg_list ? "CL" : NULL,
param->arg_list ? param->arg_list : NULL,
NULL) != 0) {
fprintf(stderr, "[ampliconclip] warning: unable to add @PG line to header.\n");
}
if (sam_hdr_write(out, header) < 0) {
fprintf(stderr, "[ampliconclip] error: could not write header.\n");
goto fail;
}
if (reject) {
if (sam_hdr_write(reject, header) < 0) {
fprintf(stderr, "[ampliconclip] error: could not write header to rejects file.\n");
goto fail;
}
}
b = bam_init1();
b_tmp = bam_init1();
if (!b || !b_tmp) {
fprintf(stderr, "[ampliconclip] error: out of memory when trying to create record.\n");
goto fail;
}
int32_t last_tid = -1;
int ref_found = 0;
while ((r = sam_read1(in, header, b)) >= 0) {
hts_pos_t pos;
int is_rev;
int p_size;
int been_clipped = 0, filter = 0;
int exclude = (BAM_FUNMAP | BAM_FQCFAIL);
khiter_t itr;
l_count++;
if (b->core.tid != last_tid) {
const char *ref_name;
ref_found = 0;
last_tid = b->core.tid;
if ((ref_name = sam_hdr_tid2name(header, b->core.tid)) != NULL) {
itr = kh_get(bed_list_hash, bed_hash, ref_name);
if (itr != kh_end(bed_hash)) {
sites = &kh_val(bed_hash, itr);
ref_found = 1;
}
}
}
if (!(b->core.flag & exclude) && ref_found) {
if (param->oa_tag)
if (tag_original_data(b, &oat))
goto fail;
if (!param->both) {
if (bam_is_rev(b)) {
pos = bam_endpos(b);
is_rev = 1;
} else {
pos = b->core.pos;
is_rev = 0;
}
if ((p_size = matching_clip_site(sites, pos, is_rev, param->use_strand, sites->longest, param))) {
if (is_rev) {
if (bam_trim_right(b, b_tmp, p_size, clipping) != 0)
goto fail;
swap_bams(&b, &b_tmp);
r_count++;
} else {
if (bam_trim_left(b, b_tmp, p_size, clipping) != 0)
goto fail;
swap_bams(&b, &b_tmp);
f_count++;
}
if (param->oa_tag) {
if (bam_aux_update_str(b, "OA", oat.l + 1, (const char *)oat.s))
goto fail;
}
if (param->del_tag) {
uint8_t *tag;
if ((tag = bam_aux_get(b, "NM")))
bam_aux_del(b, tag);
if ((tag = bam_aux_get(b, "MD")))
bam_aux_del(b, tag);
}
been_clipped = 1;
} else {
if (param->mark_fail) {
b->core.flag |= BAM_FQCFAIL;
}
n_count++;
}
} else {
int left = 0, right = 0;
// left first
pos = b->core.pos;
is_rev = 0;
if ((p_size = matching_clip_site(sites, pos, is_rev, param->use_strand, sites->longest, param))) {
if (bam_trim_left(b, b_tmp, p_size, clipping) != 0)
goto fail;
swap_bams(&b, &b_tmp);
f_count++;
left = 1;
been_clipped = 1;
}
// the right
pos = bam_endpos(b);
is_rev = 1;
if ((p_size = matching_clip_site(sites, pos, is_rev, param->use_strand, sites->longest, param))) {
if (bam_trim_right(b, b_tmp, p_size, clipping) != 0)
goto fail;
swap_bams(&b, &b_tmp);
r_count++;
right = 1;
been_clipped = 1;
}
if (left || right) {
uint8_t *tag;
if (param->oa_tag) {
if (bam_aux_update_str(b, "OA", oat.l + 1, (const char *)oat.s))
goto fail;
}
if (param->del_tag) {
if ((tag = bam_aux_get(b, "NM")))
bam_aux_del(b, tag);
if ((tag = bam_aux_get(b, "MD")))
bam_aux_del(b, tag);
}
}
if (left && right) {
b_count++;
} else if (!left && !right) {
if (param->mark_fail) {
b->core.flag |= BAM_FQCFAIL;
}
n_count++;
}
}
if (param->fail_len >= 0 || param->filter_len >= 0) {
hts_pos_t aql = active_query_len(b);
if (param->fail_len >= 0 && aql <= param->fail_len) {
b->core.flag |= BAM_FQCFAIL;
}
if (param->filter_len >= 0 && aql <= param->filter_len) {
filter = 1;
}
}
if (b->core.flag & BAM_FQCFAIL) {
failed++;
}
if (param->write_clipped && !been_clipped) {
filter = 1;
}
} else {
l_exclude++;
if (param->unmapped) {
filter = 1;
}
}
if (!filter) {
if (sam_write1(out, header, b) < 0) {
fprintf(stderr, "[ampliconclip] error: could not write line %ld.\n", l_count);
goto fail;
}
written++;
} else {
if (reject) {
if (sam_write1(reject, header, b) < 0) {
fprintf(stderr, "[ampliconclip] error: could not write to reject file %s\n",
param->rejects_file);
goto fail;
}
}
filtered++;
}
}
if (r < -1) {
fprintf(stderr, "[ampliconclip] error: failed to read input.\n");
goto fail;
}
if (param->stats_file) {
if ((stats_fp = fopen(param->stats_file, "w")) == NULL) {
fprintf(stderr, "[ampliconclip] warning: cannot write stats to %s.\n", param->stats_file);
} else {
file_open = 1;
}
}
fprintf(stats_fp, "COMMAND: %s\n"
"TOTAL READS: %ld\n"
"TOTAL CLIPPED: %ld\n"
"FORWARD CLIPPED: %ld\n"
"REVERSE CLIPPED: %ld\n"
"BOTH CLIPPED: %ld\n"
"NOT CLIPPED: %ld\n"
"EXCLUDED: %ld\n"
"FILTERED: %ld\n"
"FAILED: %ld\n"
"WRITTEN: %ld\n", param->arg_list, l_count, f_count + r_count,
f_count, r_count, b_count, n_count, l_exclude,
filtered, failed, written);
if (file_open) {
fclose(stats_fp);
}
ret = 0;
fail:
destroy_bed_hash(bed_hash);
ks_free(&oat);
sam_hdr_destroy(header);
bam_destroy1(b);
bam_destroy1(b_tmp);
return ret;
}
static void usage(void) {
fprintf(stderr, "Usage: samtools ampliconclip -b BED file <input.bam> -o <output.bam>\n\n");
fprintf(stderr, "Option: \n");
fprintf(stderr, " -b FILE BED file of regions (eg amplicon primers) to be removed.\n");
fprintf(stderr, " -o FILE output file name (default stdout).\n");
fprintf(stderr, " -f FILE write stats to file name (default stderr)\n");
fprintf(stderr, " -u Output uncompressed data\n");
fprintf(stderr, " --soft-clip soft clip amplicon primers from reads (default)\n");
fprintf(stderr, " --hard-clip hard clip amplicon primers from reads.\n");
fprintf(stderr, " --both-ends clip on both 5' and 3' ends.\n");
fprintf(stderr, " --strand use strand data from BED file to match read direction.\n");
fprintf(stderr, " --clipped only output clipped reads.\n");
fprintf(stderr, " --fail mark unclipped, mapped reads as QCFAIL.\n");
fprintf(stderr, " --filter-len INT do not output reads INT size or shorter.\n");
fprintf(stderr, " --fail-len INT mark as QCFAIL reads INT size or shorter.\n");
fprintf(stderr, " --no-excluded do not write excluded reads (unmapped or QCFAIL).\n");
fprintf(stderr, " --rejects-file FILE file to write filtered reads.\n");
fprintf(stderr, " --original for clipped entries add an OA tag with original data.\n");
fprintf(stderr, " --keep-tag for clipped entries keep the old NM and MD tags.\n");
fprintf(stderr, " --tolerance match region within this number of bases, default 5.\n");
fprintf(stderr, " --no-PG do not add an @PG line.\n");
sam_global_opt_help(stderr, "-.O..@-.");
fprintf(stderr, "\nAbout: Soft clips read alignments where they match BED file defined regions.\n"
"Default clipping is only on the 5' end.\n\n");
}
int amplicon_clip_main(int argc, char **argv) {
int c, ret;
char wmode[4] = {'w', 'b', 0, 0};
char *bedfile = NULL, *fnout = "-";
sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
htsThreadPool p = {NULL, 0};
samFile *in = NULL, *out = NULL, *reject = NULL;
clipping_type clipping = soft_clip;
cl_param_t param = {1, 0, 0, 0, 0, -1, -1, 0, 0, 1, 5, NULL, NULL, NULL};
static const struct option lopts[] = {
SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 0, '@'),
{"no-PG", no_argument, NULL, 1002},
{"soft-clip", no_argument, NULL, 1003},
{"hard-clip", no_argument, NULL, 1004},
{"strand", no_argument, NULL, 1005},
{"clipped", no_argument, NULL, 1006},
{"fail", no_argument, NULL, 1007},
{"both-ends", no_argument, NULL, 1008},
{"filter-len", required_argument, NULL, 1009},
{"fail-len", required_argument, NULL, 1010},
{"no-excluded", no_argument, NULL, 1011},
{"rejects-file", required_argument, NULL, 1012},
{"original", no_argument, NULL, 1013},
{"keep-tag", no_argument, NULL, 1014},
{"tolerance", required_argument, NULL, 1015},
{NULL, 0, NULL, 0}
};
while ((c = getopt_long(argc, argv, "b:@:o:O:f:u", lopts, NULL)) >= 0) {
switch (c) {
case 'b': bedfile = optarg; break;
case 'o': fnout = optarg; break;
case 'f': param.stats_file = optarg; break;
case 'u': wmode[2] = '0'; break;
case 1002: param.add_pg = 0; break;
case 1003: clipping = soft_clip; break;
case 1004: clipping = hard_clip; break;
case 1005: param.use_strand = 1; break;
case 1006: param.write_clipped = 1; break;
case 1007: param.mark_fail = 1; break;
case 1008: param.both = 1; break;
case 1009: param.filter_len = atoi(optarg); break;
case 1010: param.fail_len = atoi(optarg); break;
case 1011: param.unmapped = 1; break;
case 1012: param.rejects_file = optarg; break;
case 1013: param.oa_tag = 1; break;
case 1014: param.del_tag = 0; break;
case 1015: param.tol = atoi(optarg); break;
default: if (parse_sam_global_opt(c, optarg, lopts, &ga) == 0) break;
/* else fall-through */
case '?': usage(); exit(1);
}