forked from samtools/samtools
-
Notifications
You must be signed in to change notification settings - Fork 0
/
sam_view.c
1071 lines (982 loc) · 37 KB
/
sam_view.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
/* sam_view.c -- SAM<->BAM<->CRAM conversion.
Copyright (C) 2009-2017 Genome Research Ltd.
Portions copyright (C) 2009, 2011, 2012 Broad Institute.
Author: Heng Li <[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 notices 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 <stdlib.h>
#include <string.h>
#include <stdio.h>
#include <unistd.h>
#include <math.h>
#include <inttypes.h>
#include <stdbool.h>
#include <assert.h>
#include <getopt.h>
#include "htslib/sam.h"
#include "htslib/faidx.h"
#include "htslib/kstring.h"
#include "htslib/khash.h"
#include "htslib/thread_pool.h"
#include "samtools.h"
#include "sam_opts.h"
KHASH_SET_INIT_STR(rg)
typedef khash_t(rg) *rghash_t;
// This structure contains the settings for a samview run
typedef struct samview_settings {
rghash_t rghash;
int min_mapQ;
int flag_on;
int flag_off;
int min_qlen;
int remove_B;
uint32_t subsam_seed;
double subsam_frac;
char* library;
void* bed;
size_t remove_aux_len;
char** remove_aux;
} samview_settings_t;
// TODO Add declarations of these to a viable htslib or samtools header
extern const char *bam_get_library(bam_hdr_t *header, const bam1_t *b);
extern int bam_remove_B(bam1_t *b);
extern char *samfaipath(const char *fn_ref);
void *bed_read(const char *fn);
void bed_destroy(void *_h);
int bed_overlap(const void *_h, const char *chr, int beg, int end);
// Returns 0 to indicate read should be output 1 otherwise
static int process_aln(const bam_hdr_t *h, bam1_t *b, samview_settings_t* settings)
{
if (settings->remove_B) bam_remove_B(b);
if (settings->min_qlen > 0) {
int k, qlen = 0;
uint32_t *cigar = bam_get_cigar(b);
for (k = 0; k < b->core.n_cigar; ++k)
if ((bam_cigar_type(bam_cigar_op(cigar[k]))&1) || bam_cigar_op(cigar[k]) == BAM_CHARD_CLIP)
qlen += bam_cigar_oplen(cigar[k]);
if (qlen < settings->min_qlen) return 1;
}
if (b->core.qual < settings->min_mapQ || ((b->core.flag & settings->flag_on) != settings->flag_on) || (b->core.flag & settings->flag_off))
return 1;
if (settings->bed && (b->core.tid < 0 || !bed_overlap(settings->bed, h->target_name[b->core.tid], b->core.pos, bam_endpos(b))))
return 1;
if (settings->subsam_frac > 0.) {
uint32_t k = __ac_Wang_hash(__ac_X31_hash_string(bam_get_qname(b)) ^ settings->subsam_seed);
if ((double)(k&0xffffff) / 0x1000000 >= settings->subsam_frac) return 1;
}
if (settings->rghash) {
uint8_t *s = bam_aux_get(b, "RG");
if (s) {
khint_t k = kh_get(rg, settings->rghash, (char*)(s + 1));
if (k == kh_end(settings->rghash)) return 1;
}
}
if (settings->library) {
const char *p = bam_get_library((bam_hdr_t*)h, b);
if (!p || strcmp(p, settings->library) != 0) return 1;
}
if (settings->remove_aux_len) {
size_t i;
for (i = 0; i < settings->remove_aux_len; ++i) {
uint8_t *s = bam_aux_get(b, settings->remove_aux[i]);
if (s) {
bam_aux_del(b, s);
}
}
}
return 0;
}
static char *drop_rg(char *hdtxt, rghash_t h, int *len)
{
char *p = hdtxt, *q, *r, *s;
kstring_t str;
memset(&str, 0, sizeof(kstring_t));
while (1) {
int toprint = 0;
q = strchr(p, '\n');
if (q == 0) q = p + strlen(p);
if (q - p < 3) break; // the line is too short; then stop
if (strncmp(p, "@RG\t", 4) == 0) {
int c;
khint_t k;
if ((r = strstr(p, "\tID:")) != 0) {
r += 4;
for (s = r; *s != '\0' && *s != '\n' && *s != '\t'; ++s);
c = *s; *s = '\0';
k = kh_get(rg, h, r);
*s = c;
if (k != kh_end(h)) toprint = 1;
}
} else toprint = 1;
if (toprint) {
kputsn(p, q - p, &str); kputc('\n', &str);
}
p = q + 1;
}
*len = str.l;
return str.s;
}
static int usage(FILE *fp, int exit_status, int is_long_help);
static int add_read_group_single(const char *subcmd, samview_settings_t *settings, char *name)
{
char *d = strdup(name);
int ret = 0;
if (d == NULL) goto err;
if (settings->rghash == NULL) {
settings->rghash = kh_init(rg);
if (settings->rghash == NULL) goto err;
}
kh_put(rg, settings->rghash, d, &ret);
if (ret == -1) goto err;
if (ret == 0) free(d); /* Duplicate */
return 0;
err:
print_error(subcmd, "Couldn't add \"%s\" to read group list: memory exhausted?", name);
free(d);
return -1;
}
static int add_read_groups_file(const char *subcmd, samview_settings_t *settings, char *fn)
{
FILE *fp;
char buf[1024];
int ret = 0;
if (settings->rghash == NULL) {
settings->rghash = kh_init(rg);
if (settings->rghash == NULL) {
perror(NULL);
return -1;
}
}
fp = fopen(fn, "r");
if (fp == NULL) {
print_error_errno(subcmd, "failed to open \"%s\" for reading", fn);
return -1;
}
while (ret != -1 && !feof(fp) && fscanf(fp, "%1023s", buf) > 0) {
char *d = strdup(buf);
if (d != NULL) {
kh_put(rg, settings->rghash, d, &ret);
if (ret == 0) free(d); /* Duplicate */
} else {
ret = -1;
}
}
if (ferror(fp)) ret = -1;
if (ret == -1) {
print_error_errno(subcmd, "failed to read \"%s\"", fn);
}
fclose(fp);
return (ret != -1) ? 0 : -1;
}
static inline int check_sam_write1(samFile *fp, const bam_hdr_t *h, const bam1_t *b, const char *fname, int *retp)
{
int r = sam_write1(fp, h, b);
if (r >= 0) return r;
if (fname) print_error_errno("view", "writing to \"%s\" failed", fname);
else print_error_errno("view", "writing to standard output failed");
*retp = EXIT_FAILURE;
return r;
}
static void check_sam_close(const char *subcmd, samFile *fp, const char *fname, const char *null_fname, int *retp)
{
int r = sam_close(fp);
if (r >= 0) return;
// TODO Need error infrastructure so we can print a message instead of r
if (fname) print_error(subcmd, "error closing \"%s\": %d", fname, r);
else print_error(subcmd, "error closing %s: %d", null_fname, r);
*retp = EXIT_FAILURE;
}
int main_samview(int argc, char *argv[])
{
int c, is_header = 0, is_header_only = 0, ret = 0, compress_level = -1, is_count = 0;
int is_long_help = 0;
int64_t count = 0;
samFile *in = 0, *out = 0, *un_out=0;
FILE *fp_out = NULL;
bam_hdr_t *header = NULL;
char out_mode[5], out_un_mode[5], *out_format = "";
char *fn_in = 0, *fn_out = 0, *fn_list = 0, *q, *fn_un_out = 0;
sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
htsThreadPool p = {NULL, 0};
samview_settings_t settings = {
.rghash = NULL,
.min_mapQ = 0,
.flag_on = 0,
.flag_off = 0,
.min_qlen = 0,
.remove_B = 0,
.subsam_seed = 0,
.subsam_frac = -1.,
.library = NULL,
.bed = NULL,
};
static const struct option lopts[] = {
SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 'T', '@'),
{ NULL, 0, NULL, 0 }
};
/* parse command-line options */
strcpy(out_mode, "w");
strcpy(out_un_mode, "w");
while ((c = getopt_long(argc, argv,
"SbBcCt:h1Ho:O:q:f:F:ul:r:?T:R:L:s:@:m:x:U:",
lopts, NULL)) >= 0) {
switch (c) {
case 's':
if ((settings.subsam_seed = strtol(optarg, &q, 10)) != 0) {
// Convert likely user input 0,1,2,... to pseudo-random
// values with more entropy and more bits set
srand(settings.subsam_seed);
settings.subsam_seed = rand();
}
settings.subsam_frac = strtod(q, &q);
break;
case 'm': settings.min_qlen = atoi(optarg); break;
case 'c': is_count = 1; break;
case 'S': break;
case 'b': out_format = "b"; break;
case 'C': out_format = "c"; break;
case 't': fn_list = strdup(optarg); break;
case 'h': is_header = 1; break;
case 'H': is_header_only = 1; break;
case 'o': fn_out = strdup(optarg); break;
case 'U': fn_un_out = strdup(optarg); break;
case 'f': settings.flag_on |= strtol(optarg, 0, 0); break;
case 'F': settings.flag_off |= strtol(optarg, 0, 0); break;
case 'q': settings.min_mapQ = atoi(optarg); break;
case 'u': compress_level = 0; break;
case '1': compress_level = 1; break;
case 'l': settings.library = strdup(optarg); break;
case 'L':
if ((settings.bed = bed_read(optarg)) == NULL) {
print_error_errno("view", "Could not read file \"%s\"", optarg);
ret = 1;
goto view_end;
}
break;
case 'r':
if (add_read_group_single("view", &settings, optarg) != 0) {
ret = 1;
goto view_end;
}
break;
case 'R':
if (add_read_groups_file("view", &settings, optarg) != 0) {
ret = 1;
goto view_end;
}
break;
/* REMOVED as htslib doesn't support this
//case 'x': out_format = "x"; break;
//case 'X': out_format = "X"; break;
*/
case '?': is_long_help = 1; break;
case 'B': settings.remove_B = 1; break;
case 'x':
{
if (strlen(optarg) != 2) {
fprintf(stderr, "main_samview: Error parsing -x auxiliary tags should be exactly two characters long.\n");
return usage(stderr, EXIT_FAILURE, is_long_help);
}
settings.remove_aux = (char**)realloc(settings.remove_aux, sizeof(char*) * (++settings.remove_aux_len));
settings.remove_aux[settings.remove_aux_len-1] = optarg;
}
break;
default:
if (parse_sam_global_opt(c, optarg, lopts, &ga) != 0)
return usage(stderr, EXIT_FAILURE, is_long_help);
break;
}
}
if (compress_level >= 0 && !*out_format) out_format = "b";
if (is_header_only) is_header = 1;
// File format auto-detection first
if (fn_out) sam_open_mode(out_mode+1, fn_out, NULL);
if (fn_un_out) sam_open_mode(out_un_mode+1, fn_un_out, NULL);
// Overridden by manual -b, -C
if (*out_format)
out_mode[1] = out_un_mode[1] = *out_format;
out_mode[2] = out_un_mode[2] = '\0';
// out_(un_)mode now 1 or 2 bytes long, followed by nul.
if (compress_level >= 0) {
char tmp[2];
tmp[0] = compress_level + '0'; tmp[1] = '\0';
strcat(out_mode, tmp);
strcat(out_un_mode, tmp);
}
if (argc == optind && isatty(STDIN_FILENO)) return usage(stdout, EXIT_SUCCESS, is_long_help); // potential memory leak...
fn_in = (optind < argc)? argv[optind] : "-";
// generate the fn_list if necessary
if (fn_list == 0 && ga.reference) fn_list = samfaipath(ga.reference);
// open file handlers
if ((in = sam_open_format(fn_in, "r", &ga.in)) == 0) {
print_error_errno("view", "failed to open \"%s\" for reading", fn_in);
ret = 1;
goto view_end;
}
if (fn_list) {
if (hts_set_fai_filename(in, fn_list) != 0) {
fprintf(stderr, "[main_samview] failed to use reference \"%s\".\n", fn_list);
ret = 1;
goto view_end;
}
}
if ((header = sam_hdr_read(in)) == 0) {
fprintf(stderr, "[main_samview] fail to read the header from \"%s\".\n", fn_in);
ret = 1;
goto view_end;
}
if (settings.rghash) { // FIXME: I do not know what "bam_header_t::n_text" is for...
char *tmp;
int l;
tmp = drop_rg(header->text, settings.rghash, &l);
free(header->text);
header->text = tmp;
header->l_text = l;
}
if (!is_count) {
if ((out = sam_open_format(fn_out? fn_out : "-", out_mode, &ga.out)) == 0) {
print_error_errno("view", "failed to open \"%s\" for writing", fn_out? fn_out : "standard output");
ret = 1;
goto view_end;
}
if (fn_list) {
if (hts_set_fai_filename(out, fn_list) != 0) {
fprintf(stderr, "[main_samview] failed to use reference \"%s\".\n", fn_list);
ret = 1;
goto view_end;
}
}
if (*out_format || is_header ||
out_mode[1] == 'b' || out_mode[1] == 'c' ||
(ga.out.format != sam && ga.out.format != unknown_format)) {
if (sam_hdr_write(out, header) != 0) {
fprintf(stderr, "[main_samview] failed to write the SAM header\n");
ret = 1;
goto view_end;
}
}
if (fn_un_out) {
if ((un_out = sam_open_format(fn_un_out, out_un_mode, &ga.out)) == 0) {
print_error_errno("view", "failed to open \"%s\" for writing", fn_un_out);
ret = 1;
goto view_end;
}
if (fn_list) {
if (hts_set_fai_filename(un_out, fn_list) != 0) {
fprintf(stderr, "[main_samview] failed to use reference \"%s\".\n", fn_list);
ret = 1;
goto view_end;
}
}
if (*out_format || is_header ||
out_un_mode[1] == 'b' || out_un_mode[1] == 'c' ||
(ga.out.format != sam && ga.out.format != unknown_format)) {
if (sam_hdr_write(un_out, header) != 0) {
fprintf(stderr, "[main_samview] failed to write the SAM header\n");
ret = 1;
goto view_end;
}
}
}
}
else {
if (fn_out) {
fp_out = fopen(fn_out, "w");
if (fp_out == NULL) {
print_error_errno("view", "can't create \"%s\"", fn_out);
ret = EXIT_FAILURE;
goto view_end;
}
}
}
if (ga.nthreads > 1) {
if (!(p.pool = hts_tpool_init(ga.nthreads))) {
fprintf(stderr, "Error creating thread pool\n");
ret = 1;
goto view_end;
}
hts_set_opt(in, HTS_OPT_THREAD_POOL, &p);
if (out) hts_set_opt(out, HTS_OPT_THREAD_POOL, &p);
}
if (is_header_only) goto view_end; // no need to print alignments
if (optind + 1 >= argc) { // convert/print the entire file
bam1_t *b = bam_init1();
int r;
while ((r = sam_read1(in, header, b)) >= 0) { // read one alignment from `in'
if (!process_aln(header, b, &settings)) {
if (!is_count) { if (check_sam_write1(out, header, b, fn_out, &ret) < 0) break; }
count++;
} else {
if (un_out) { if (check_sam_write1(un_out, header, b, fn_un_out, &ret) < 0) break; }
}
}
if (r < -1) {
fprintf(stderr, "[main_samview] truncated file.\n");
ret = 1;
}
bam_destroy1(b);
} else { // retrieve alignments in specified regions
int i;
bam1_t *b;
hts_idx_t *idx = sam_index_load(in, fn_in); // load index
if (idx == 0) { // index is unavailable
fprintf(stderr, "[main_samview] random alignment retrieval only works for indexed BAM or CRAM files.\n");
ret = 1;
goto view_end;
}
b = bam_init1();
for (i = optind + 1; i < argc; ++i) {
int result;
hts_itr_t *iter = sam_itr_querys(idx, header, argv[i]); // parse a region in the format like `chr2:100-200'
if (iter == NULL) { // region invalid or reference name not found
int beg, end;
if (hts_parse_reg(argv[i], &beg, &end))
fprintf(stderr, "[main_samview] region \"%s\" specifies an unknown reference name. Continue anyway.\n", argv[i]);
else
fprintf(stderr, "[main_samview] region \"%s\" could not be parsed. Continue anyway.\n", argv[i]);
continue;
}
// fetch alignments
while ((result = sam_itr_next(in, iter, b)) >= 0) {
if (!process_aln(header, b, &settings)) {
if (!is_count) { if (check_sam_write1(out, header, b, fn_out, &ret) < 0) break; }
count++;
} else {
if (un_out) { if (check_sam_write1(un_out, header, b, fn_un_out, &ret) < 0) break; }
}
}
hts_itr_destroy(iter);
if (result < -1) {
fprintf(stderr, "[main_samview] retrieval of region \"%s\" failed due to truncated file or corrupt BAM index file\n", argv[i]);
ret = 1;
break;
}
}
bam_destroy1(b);
hts_idx_destroy(idx); // destroy the BAM index
}
view_end:
if (is_count && ret == 0) {
if (fprintf(fn_out? fp_out : stdout, "%" PRId64 "\n", count) < 0) {
if (fn_out) print_error_errno("view", "writing to \"%s\" failed", fn_out);
else print_error_errno("view", "writing to standard output failed");
ret = EXIT_FAILURE;
}
}
// close files, free and return
if (in) check_sam_close("view", in, fn_in, "standard input", &ret);
if (out) check_sam_close("view", out, fn_out, "standard output", &ret);
if (un_out) check_sam_close("view", un_out, fn_un_out, "file", &ret);
if (fp_out) fclose(fp_out);
free(fn_list); free(fn_out); free(settings.library); free(fn_un_out);
sam_global_args_free(&ga);
if ( header ) bam_hdr_destroy(header);
if (settings.bed) bed_destroy(settings.bed);
if (settings.rghash) {
khint_t k;
for (k = 0; k < kh_end(settings.rghash); ++k)
if (kh_exist(settings.rghash, k)) free((char*)kh_key(settings.rghash, k));
kh_destroy(rg, settings.rghash);
}
if (settings.remove_aux_len) {
free(settings.remove_aux);
}
if (p.pool)
hts_tpool_destroy(p.pool);
return ret;
}
static int usage(FILE *fp, int exit_status, int is_long_help)
{
fprintf(fp,
"\n"
"Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region ...]\n"
"\n"
"Options:\n"
// output options
" -b output BAM\n"
" -C output CRAM (requires -T)\n"
" -1 use fast BAM compression (implies -b)\n"
" -u uncompressed BAM output (implies -b)\n"
" -h include header in SAM output\n"
" -H print SAM header only (no alignments)\n"
" -c print only the count of matching records\n"
" -o FILE output file name [stdout]\n"
" -U FILE output reads not selected by filters to FILE [null]\n"
// extra input
" -t FILE FILE listing reference names and lengths (see long help) [null]\n"
// read filters
" -L FILE only include reads overlapping this BED FILE [null]\n"
" -r STR only include reads in read group STR [null]\n"
" -R FILE only include reads with read group listed in FILE [null]\n"
" -q INT only include reads with mapping quality >= INT [0]\n"
" -l STR only include reads in library STR [null]\n"
" -m INT only include reads with number of CIGAR operations consuming\n"
" query sequence >= INT [0]\n"
" -f INT only include reads with all bits set in INT set in FLAG [0]\n"
" -F INT only include reads with none of the bits set in INT set in FLAG [0]\n"
" -s FLOAT subsample reads (given INT.FRAC option value, 0.FRAC is the\n"
" fraction of templates/read pairs to keep; INT part sets seed)\n"
// read processing
" -x STR read tag to strip (repeatable) [null]\n"
" -B collapse the backward CIGAR operation\n"
// general options
" -? print long help, including note about region specification\n"
" -S ignored (input format is auto-detected)\n");
sam_global_opt_help(fp, "-.O.T@");
fprintf(fp, "\n");
if (is_long_help)
fprintf(fp,
"Notes:\n"
"\n"
"1. This command now auto-detects the input format (BAM/CRAM/SAM).\n"
" Further control over the CRAM format can be specified by using the\n"
" --output-fmt-option, e.g. to specify the number of sequences per slice\n"
" and to use avoid reference based compression:\n"
"\n"
"\tsamtools view -C --output-fmt-option seqs_per_slice=5000 \\\n"
"\t --output-fmt-option no_ref -o out.cram in.bam\n"
"\n"
" Options can also be specified as a comma separated list within the\n"
" --output-fmt value too. For example this is equivalent to the above\n"
"\n"
"\tsamtools view --output-fmt cram,seqs_per_slice=5000,no_ref \\\n"
"\t -o out.cram in.bam\n"
"\n"
"2. The file supplied with `-t' is SPACE/TAB delimited with the first\n"
" two fields of each line consisting of the reference name and the\n"
" corresponding sequence length. The `.fai' file generated by \n"
" `samtools faidx' is suitable for use as this file. This may be an\n"
" empty file if reads are unaligned.\n"
"\n"
"3. SAM->BAM conversion: samtools view -bT ref.fa in.sam.gz\n"
"\n"
"4. BAM->SAM conversion: samtools view -h in.bam\n"
"\n"
"5. A region should be presented in one of the following formats:\n"
" `chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is\n"
" specified, the input alignment file must be a sorted and indexed\n"
" alignment (BAM/CRAM) file.\n"
"\n"
"6. Option `-u' is preferred over `-b' when the output is piped to\n"
" another samtools command.\n"
"\n");
return exit_status;
}
int main_import(int argc, char *argv[])
{
int argc2, ret;
char **argv2;
if (argc != 4) {
fprintf(stderr, "Usage: samtools import <in.ref_list> <in.sam> <out.bam>\n");
return 1;
}
argc2 = 6;
argv2 = calloc(6, sizeof(char*));
argv2[0] = "import", argv2[1] = "-o", argv2[2] = argv[3], argv2[3] = "-bt", argv2[4] = argv[1], argv2[5] = argv[2];
ret = main_samview(argc2, argv2);
free(argv2);
return ret;
}
int8_t seq_comp_table[16] = { 0, 8, 4, 12, 2, 10, 6, 14, 1, 9, 5, 13, 3, 11, 7, 15 };
static const char *copied_tags[] = { "RG", "BC", "QT", NULL };
static void bam2fq_usage(FILE *to, const char *command)
{
int fq = strcasecmp("fastq", command) == 0 || strcasecmp("bam2fq", command) == 0;
fprintf(to,
"Usage: samtools %s [options...] <in.bam>\n", command);
fprintf(to,
"Options:\n"
" -0 FILE write paired reads flagged both or neither READ1 and READ2 to FILE\n"
" -1 FILE write paired reads flagged READ1 to FILE\n"
" -2 FILE write paired reads flagged READ2 to FILE\n"
" -f INT only include reads with all bits set in INT set in FLAG [0]\n"
" -F INT only include reads with none of the bits set in INT set in FLAG [0]\n"
" -n don't append /1 and /2 to the read name\n");
if (fq) fprintf(to,
" -O output quality in the OQ tag if present\n");
fprintf(to,
" -s FILE write singleton reads to FILE [assume single-end]\n"
" -t copy RG, BC and QT tags to the %s header line\n",
fq ? "FASTQ" : "FASTA");
if (fq) fprintf(to,
" -v INT default quality score if not given in file [1]\n");
sam_global_opt_help(to, "-.--.@");
}
typedef enum { READ_UNKNOWN = 0, READ_1 = 1, READ_2 = 2 } readpart;
typedef enum { FASTA, FASTQ } fastfile;
typedef struct bam2fq_opts {
char *fnse;
char *fnr[3];
char *fn_input; // pointer to input filename in argv do not free
bool has12, use_oq, copy_tags;
int flag_on, flag_off;
sam_global_args ga;
fastfile filetype;
int def_qual;
} bam2fq_opts_t;
typedef struct bam2fq_state {
samFile *fp;
FILE *fpse;
FILE *fpr[3];
bam_hdr_t *h;
bool has12, use_oq, copy_tags;
int flag_on, flag_off;
fastfile filetype;
int def_qual;
} bam2fq_state_t;
static readpart which_readpart(const bam1_t *b)
{
if ((b->core.flag & BAM_FREAD1) && !(b->core.flag & BAM_FREAD2)) {
return READ_1;
} else if ((b->core.flag & BAM_FREAD2) && !(b->core.flag & BAM_FREAD1)) {
return READ_2;
} else {
return READ_UNKNOWN;
}
}
// Transform a bam1_t record into a string with the FASTQ representation of it
// @returns false for error, true for success
static bool bam1_to_fq(const bam1_t *b, kstring_t *linebuf, const bam2fq_state_t *state)
{
int i;
int32_t qlen = b->core.l_qseq;
assert(qlen >= 0);
uint8_t *seq;
uint8_t *qual = bam_get_qual(b);
const uint8_t *oq = NULL;
if (state->use_oq) {
oq = bam_aux_get(b, "OQ");
if (oq) oq++; // skip tag type
}
bool has_qual = (qual[0] != 0xff || (state->use_oq && oq)); // test if there is quality
linebuf->l = 0;
// Write read name
readpart readpart = which_readpart(b);
kputc(state->filetype == FASTA? '>' : '@', linebuf);
kputs(bam_get_qname(b), linebuf);
// Add the /1 /2 if requested
if (state->has12) {
if (readpart == READ_1) kputs("/1", linebuf);
else if (readpart == READ_2) kputs("/2", linebuf);
}
if (state->copy_tags) {
for (i = 0; copied_tags[i]; ++i) {
uint8_t *s;
if ((s = bam_aux_get(b, copied_tags[i])) != 0) {
kputc('\t', linebuf);
kputsn(copied_tags[i], 2, linebuf);
kputsn(":Z:", 3, linebuf);
kputs(bam_aux2Z(s), linebuf);
}
}
}
kputc('\n', linebuf);
seq = bam_get_seq(b);
if (b->core.flag & BAM_FREVERSE) { // read is reverse complemented
for (i = qlen-1; i > -1; --i) {
char c = seq_nt16_str[seq_comp_table[bam_seqi(seq,i)]];
kputc(c, linebuf);
}
} else {
for (i = 0; i < qlen; ++i) {
char c = seq_nt16_str[bam_seqi(seq,i)];
kputc(c, linebuf);
}
}
kputc('\n', linebuf);
if (state->filetype == FASTQ) {
// Write quality
kputs("+\n", linebuf);
if (has_qual) {
if (state->use_oq && oq) {
if (b->core.flag & BAM_FREVERSE) { // read is reverse complemented
for (i = qlen-1; i > -1; --i) {
kputc(oq[i], linebuf);
}
} else {
kputs((char*)oq, linebuf);
}
} else {
if (b->core.flag & BAM_FREVERSE) { // read is reverse complemented
for (i = qlen-1; i > -1; --i) {
kputc(33 + qual[i], linebuf);
}
} else {
for (i = 0; i < qlen; ++i) {
kputc(33 + qual[i], linebuf);
}
}
}
} else {
for (i = 0; i < qlen; ++i) {
kputc(33 + state->def_qual, linebuf);
}
}
kputc('\n', linebuf);
}
return true;
}
// return true if valid
static bool parse_opts(int argc, char *argv[], bam2fq_opts_t** opts_out)
{
// Parse args
bam2fq_opts_t* opts = calloc(1, sizeof(bam2fq_opts_t));
opts->has12 = true;
opts->filetype = FASTQ;
opts->def_qual = 1;
int c;
sam_global_args_init(&opts->ga);
static const struct option lopts[] = {
SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0, '@'),
{ NULL, 0, NULL, 0 }
};
while ((c = getopt_long(argc, argv, "0:1:2:f:F:nOs:tv:@:", lopts, NULL)) > 0) {
switch (c) {
case '0': opts->fnr[0] = optarg; break;
case '1': opts->fnr[1] = optarg; break;
case '2': opts->fnr[2] = optarg; break;
case 'f': opts->flag_on |= strtol(optarg, 0, 0); break;
case 'F': opts->flag_off |= strtol(optarg, 0, 0); break;
case 'n': opts->has12 = false; break;
case 'O': opts->use_oq = true; break;
case 's': opts->fnse = optarg; break;
case 't': opts->copy_tags = true; break;
case 'v': opts->def_qual = atoi(optarg); break;
case '?': bam2fq_usage(stderr, argv[0]); free(opts); return false;
default:
if (parse_sam_global_opt(c, optarg, lopts, &opts->ga) != 0) {
bam2fq_usage(stderr, argv[0]); free(opts); return false;
}
break;
}
}
if (opts->fnr[1] || opts->fnr[2]) opts->has12 = false;
if (opts->def_qual < 0 || 93 < opts->def_qual) {
fprintf(stderr, "Invalid -v default quality %i, allowed range 0 to 93\n", opts->def_qual);
bam2fq_usage(stderr, argv[0]);
free(opts);
return true;
}
const char* type_str = argv[0];
if (strcasecmp("fastq", type_str) == 0 || strcasecmp("bam2fq", type_str) == 0) {
opts->filetype = FASTQ;
} else if (strcasecmp("fasta", type_str) == 0) {
opts->filetype = FASTA;
} else {
print_error("bam2fq", "Unrecognised type call \"%s\", this should be impossible... but you managed it!", type_str);
bam2fq_usage(stderr, argv[0]);
free(opts);
return false;
}
if ((argc - (optind)) == 0) {
bam2fq_usage(stdout, argv[0]);
free(opts);
return false;
}
if ((argc - (optind)) != 1) {
fprintf(stderr, "Too many arguments.\n");
bam2fq_usage(stderr, argv[0]);
free(opts);
return false;
}
opts->fn_input = argv[optind];
*opts_out = opts;
return true;
}
static bool init_state(const bam2fq_opts_t* opts, bam2fq_state_t** state_out)
{
bam2fq_state_t* state = calloc(1, sizeof(bam2fq_state_t));
state->flag_on = opts->flag_on;
state->flag_off = opts->flag_off;
state->has12 = opts->has12;
state->use_oq = opts->use_oq;
state->copy_tags = opts->copy_tags;
state->filetype = opts->filetype;
state->def_qual = opts->def_qual;
state->fp = sam_open(opts->fn_input, "r");
if (state->fp == NULL) {
print_error_errno("bam2fq","Cannot read file \"%s\"", opts->fn_input);
free(state);
return false;
}
if (opts->ga.nthreads > 0)
hts_set_threads(state->fp, opts->ga.nthreads);
uint32_t rf = SAM_QNAME | SAM_FLAG | SAM_SEQ | SAM_QUAL;
if (opts->use_oq) rf |= SAM_AUX;
if (hts_set_opt(state->fp, CRAM_OPT_REQUIRED_FIELDS, rf)) {
fprintf(stderr, "Failed to set CRAM_OPT_REQUIRED_FIELDS value\n");
free(state);
return false;
}
if (hts_set_opt(state->fp, CRAM_OPT_DECODE_MD, 0)) {
fprintf(stderr, "Failed to set CRAM_OPT_DECODE_MD value\n");
free(state);
return false;
}
if (opts->fnse) {
state->fpse = fopen(opts->fnse,"w");
if (state->fpse == NULL) {
print_error_errno("bam2fq", "Cannot write to singleton file \"%s\"", opts->fnse);
free(state);
return false;
}
}
int i;
for (i = 0; i < 3; ++i) {
if (opts->fnr[i]) {
state->fpr[i] = fopen(opts->fnr[i], "w");
if (state->fpr[i] == NULL) {
print_error_errno("bam2fq", "Cannot write to r%d file \"%s\"", i, opts->fnr[i]);
free(state);
return false;
}
} else {
state->fpr[i] = stdout;
}
}
state->h = sam_hdr_read(state->fp);
if (state->h == NULL) {
fprintf(stderr, "Failed to read header for \"%s\"\n", opts->fn_input);
free(state);
return false;
}
*state_out = state;
return true;
}
static bool destroy_state(const bam2fq_opts_t *opts, bam2fq_state_t *state, int* status)
{
bool valid = true;
bam_hdr_destroy(state->h);
check_sam_close("bam2fq", state->fp, opts->fn_input, "file", status);
if (state->fpse && fclose(state->fpse)) { print_error_errno("bam2fq", "Error closing singleton file \"%s\"", opts->fnse); valid = false; }
int i;
for (i = 0; i < 3; ++i) {
if (state->fpr[i] != stdout && fclose(state->fpr[i])) { print_error_errno("bam2fq", "Error closing r%d file \"%s\"", i, opts->fnr[i]); valid = false; }
}
free(state);
return valid;
}
static inline bool filter_it_out(const bam1_t *b, const bam2fq_state_t *state)
{
return (b->core.flag&(BAM_FSECONDARY|BAM_FSUPPLEMENTARY) // skip secondary and supplementary alignments
|| (b->core.flag&(state->flag_on)) != state->flag_on // or reads indicated by filter flags
|| (b->core.flag&(state->flag_off)) != 0);
}
static bool bam2fq_mainloop_singletontrack(bam2fq_state_t *state)
{
bam1_t* b = bam_init1();
char *current_qname = NULL;
int64_t n_reads = 0, n_singletons = 0; // Statistics
kstring_t linebuf[3] = {{0,0,NULL},{0,0,NULL},{0,0,NULL}};
int score[3];
int at_eof;
if (b == NULL ) {
perror("[bam2fq_mainloop_singletontrack] Malloc error for bam record buffer.");
return false;
}
bool valid = true;
while (true) {
at_eof = sam_read1(state->fp, state->h, b) < 0;
if (!at_eof && filter_it_out(b, state)) continue;
if (!at_eof) ++n_reads;
if (at_eof || !current_qname || (strcmp(current_qname, bam_get_qname(b)) != 0)) {
if (current_qname) {
if (score[1] > 0 && score[2] > 0) {
// print linebuf[1] to fpr[1], linebuf[2] to fpr[2]
if (fputs(linebuf[1].s, state->fpr[1]) == EOF) { valid = false; break; }
if (fputs(linebuf[2].s, state->fpr[2]) == EOF) { valid = false; break; }
} else if (score[1] > 0 || score[2] > 0) {
// print whichever one exists to fpse
if (score[1] > 0) {
if (fputs(linebuf[1].s, state->fpse) == EOF) { valid = false; break; }
} else {
if (fputs(linebuf[2].s, state->fpse) == EOF) { valid = false; break; }
}
++n_singletons;
}
if (score[0]) { // TODO: check this
// print linebuf[0] to fpr[0]
if (fputs(linebuf[0].s, state->fpr[0]) == EOF) { valid = false; break; }
}
}
if (at_eof) break;
free(current_qname);
current_qname = strdup(bam_get_qname(b));
score[0] = score[1] = score[2] = 0;
}
// Prefer a copy of the read that has base qualities