forked from samtools/samtools
-
Notifications
You must be signed in to change notification settings - Fork 0
/
bam_plcmd.c
1498 lines (1395 loc) · 62.3 KB
/
bam_plcmd.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_plcmd.c -- mpileup subcommand.
Copyright (C) 2008-2015, 2019-2021 Genome Research Ltd.
Portions copyright (C) 2009-2012 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 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 <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <ctype.h>
#include <string.h>
#include <strings.h>
#include <limits.h>
#include <errno.h>
#include <sys/stat.h>
#include <getopt.h>
#include <inttypes.h>
#include <htslib/sam.h>
#include <htslib/faidx.h>
#include <htslib/kstring.h>
#include <htslib/klist.h>
#include <htslib/khash_str2int.h>
#include <htslib/cram.h>
#include "samtools.h"
#include "bedidx.h"
#include "sam_opts.h"
#define dummy_free(p)
KLIST_INIT(auxlist, char *, dummy_free)
static inline int printw(int c, FILE *fp)
{
char buf[16];
int l, x;
if (c == 0) return fputc('0', fp);
for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
if (c < 0) buf[l++] = '-';
buf[l] = 0;
for (x = 0; x < l/2; ++x) {
int y = buf[x]; buf[x] = buf[l-1-x]; buf[l-1-x] = y;
}
fputs(buf, fp);
return 0;
}
static inline int pileup_seq(FILE *fp, const bam_pileup1_t *p, hts_pos_t pos,
hts_pos_t ref_len, const char *ref, kstring_t *ks,
int rev_del, int no_ins, int no_ins_mods,
int no_del, int no_ends)
{
no_ins_mods |= no_ins;
int j;
hts_base_mod_state *m = p->cd.p;
if (!no_ends && p->is_head) {
putc('^', fp);
putc(p->b->core.qual > 93? 126 : p->b->core.qual + 33, fp);
}
if (!p->is_del) {
int c = p->qpos < p->b->core.l_qseq
? seq_nt16_str[bam_seqi(bam_get_seq(p->b), p->qpos)]
: 'N';
if (ref) {
int rb = pos < ref_len? ref[pos] : 'N';
if (c == '=' || seq_nt16_table[c] == seq_nt16_table[rb]) c = bam_is_rev(p->b)? ',' : '.';
else c = bam_is_rev(p->b)? tolower(c) : toupper(c);
} else {
if (c == '=') c = bam_is_rev(p->b)? ',' : '.';
else c = bam_is_rev(p->b)? tolower(c) : toupper(c);
}
putc(c, fp);
if (m) {
int nm;
hts_base_mod mod[256];
if ((nm = bam_mods_at_qpos(p->b, p->qpos, m, mod, 256)) > 0) {
putc('[', fp);
int j;
for (j = 0; j < nm && j < 256; j++) {
char qual[20];
if (mod[j].qual >= 0)
sprintf(qual, "%d", mod[j].qual);
else
*qual = 0;
if (mod[j].modified_base < 0)
// ChEBI
fprintf(fp, "%c(%d)%s", "+-"[mod[j].strand],
-mod[j].modified_base, qual);
else
fprintf(fp, "%c%c%s", "+-"[mod[j].strand],
mod[j].modified_base, qual);
}
putc(']', fp);
}
}
} else putc(p->is_refskip? (bam_is_rev(p->b)? '<' : '>') : ((bam_is_rev(p->b) && rev_del) ? '#' : '*'), fp);
int del_len = -p->indel;
if (p->indel > 0) {
int len = bam_plp_insertion_mod(p, m && !no_ins_mods ? m : NULL,
ks, &del_len);
if (len < 0) {
print_error("mpileup", "bam_plp_insertion() failed");
return -1;
}
if (no_ins < 2) {
putc('+', fp);
printw(len, fp);
}
if (!no_ins) {
if (bam_is_rev(p->b)) {
char pad = rev_del ? '#' : '*';
int in_mod = 0;
for (j = 0; j < ks->l; j++) {
if (ks->s[j] == '[') in_mod = 1;
else if (ks->s[j] == ']') in_mod = 0;
putc(ks->s[j] != '*'
? (in_mod ? ks->s[j] : tolower(ks->s[j]))
: pad, fp);
}
} else {
int in_mod = 0;
for (j = 0; j < ks->l; j++) {
if (ks->s[j] == '[') in_mod = 1;
if (ks->s[j] == ']') in_mod = 0;
putc(in_mod ? ks->s[j] : toupper(ks->s[j]), fp);
}
}
}
}
if (del_len > 0) {
if (no_del < 2)
printw(-del_len, fp);
if (!no_del) {
for (j = 1; j <= del_len; ++j) {
int c = (ref && (int)pos+j < ref_len)? ref[pos+j] : 'N';
putc(bam_is_rev(p->b)? tolower(c) : toupper(c), fp);
}
}
}
if (!no_ends && p->is_tail) putc('$', fp);
return 0;
}
#include <assert.h>
#include "bam2bcf.h"
#include "sample.h"
#define MPLP_BCF 1
#define MPLP_VCF (1<<1)
#define MPLP_NO_COMP (1<<2)
#define MPLP_NO_ORPHAN (1<<3)
#define MPLP_REALN (1<<4)
#define MPLP_NO_INDEL (1<<5)
#define MPLP_REDO_BAQ (1<<6)
#define MPLP_ILLUMINA13 (1<<7)
#define MPLP_IGNORE_RG (1<<8)
#define MPLP_PER_SAMPLE (1<<9)
#define MPLP_SMART_OVERLAPS (1<<10)
#define MPLP_PRINT_MAPQ_CHAR (1<<11)
#define MPLP_PRINT_QPOS (1<<12)
#define MPLP_PRINT_QNAME (1<<13)
#define MPLP_PRINT_FLAG (1<<14)
#define MPLP_PRINT_RNAME (1<<15)
#define MPLP_PRINT_POS (1<<16)
#define MPLP_PRINT_MAPQ (1<<17)
#define MPLP_PRINT_CIGAR (1<<18)
#define MPLP_PRINT_RNEXT (1<<19)
#define MPLP_PRINT_PNEXT (1<<20)
#define MPLP_PRINT_TLEN (1<<21)
#define MPLP_PRINT_SEQ (1<<22)
#define MPLP_PRINT_QUAL (1<<23)
#define MPLP_PRINT_MODS (1<<24)
#define MPLP_PRINT_QPOS5 (1<<25)
#define MPLP_PRINT_LAST (1<<26) // terminator for loop
#define MPLP_MAX_DEPTH 8000
#define MPLP_MAX_INDEL_DEPTH 250
typedef struct {
int min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, fmt_flag, all, rev_del;
int rflag_require, rflag_filter;
int openQ, extQ, tandemQ, min_support; // for indels
double min_frac; // for indels
char *reg, *pl_list, *fai_fname, *output_fname;
faidx_t *fai;
void *bed, *rghash, *auxlist;
int argc;
char **argv;
char sep, empty, no_ins, no_ins_mods, no_del, no_ends;
sam_global_args ga;
} mplp_conf_t;
typedef struct {
char *ref[2];
int ref_id[2];
hts_pos_t ref_len[2];
} mplp_ref_t;
#define MPLP_REF_INIT {{NULL,NULL},{-1,-1},{0,0}}
typedef struct {
samFile *fp;
hts_itr_t *iter;
sam_hdr_t *h;
mplp_ref_t *ref;
const mplp_conf_t *conf;
} mplp_aux_t;
typedef struct {
int n;
int *n_plp, *m_plp;
bam_pileup1_t **plp;
} mplp_pileup_t;
static int build_auxlist(mplp_conf_t *conf, char *optstring) {
if (!optstring)
return 0;
void *colhash = khash_str2int_init();
if (!colhash)
return 1;
struct active_cols {
char *name;
int supported;
};
const struct active_cols colnames[11] = {
{"QNAME", 1}, {"FLAG", 1}, {"RNAME", 1}, {"POS", 1}, {"MAPQ", 1}, {"CIGAR", 0}, {"RNEXT", 1}, {"PNEXT", 1}, {"TLEN", 0}, {"SEQ", 0}, {"QUAL", 0}
};
int i, f = MPLP_PRINT_QNAME, colno = 11;
for (i = 0; i < colno; i++, f <<= 1)
if (colnames[i].supported)
khash_str2int_set(colhash, colnames[i].name, f);
conf->auxlist = kl_init(auxlist);
if (!conf->auxlist)
return 1;
char *save_p;
char *tag = strtok_r(optstring, ",", &save_p);
while (tag) {
if (khash_str2int_get(colhash, tag, &f) == 0) {
conf->flag |= f;
} else {
if (strlen(tag) != 2) {
fprintf(stderr, "[%s] tag '%s' has more than two characters or not supported\n", __func__, tag);
} else {
char **tag_p = kl_pushp(auxlist, conf->auxlist);
*tag_p = tag;
}
}
tag = strtok_r(NULL, ",", &save_p);
}
khash_str2int_destroy(colhash);
return 0;
}
static int mplp_get_ref(mplp_aux_t *ma, int tid, char **ref, hts_pos_t *ref_len) {
mplp_ref_t *r = ma->ref;
//printf("get ref %d {%d/%p, %d/%p}\n", tid, r->ref_id[0], r->ref[0], r->ref_id[1], r->ref[1]);
if (!r || !ma->conf->fai) {
*ref = NULL;
return 0;
}
// Do we need to reference count this so multiple mplp_aux_t can
// track which references are in use?
// For now we just cache the last two. Sufficient?
if (tid == r->ref_id[0]) {
*ref = r->ref[0];
*ref_len = r->ref_len[0];
return 1;
}
if (tid == r->ref_id[1]) {
// Last, swap over
int tmp_id;
hts_pos_t tmp_len;
tmp_id = r->ref_id[0]; r->ref_id[0] = r->ref_id[1]; r->ref_id[1] = tmp_id;
tmp_len = r->ref_len[0]; r->ref_len[0] = r->ref_len[1]; r->ref_len[1] = tmp_len;
char *tc;
tc = r->ref[0]; r->ref[0] = r->ref[1]; r->ref[1] = tc;
*ref = r->ref[0];
*ref_len = r->ref_len[0];
return 1;
}
// New, so migrate to old and load new
free(r->ref[1]);
r->ref[1] = r->ref[0];
r->ref_id[1] = r->ref_id[0];
r->ref_len[1] = r->ref_len[0];
r->ref_id[0] = tid;
r->ref[0] = faidx_fetch_seq64(ma->conf->fai,
sam_hdr_tid2name(ma->h, r->ref_id[0]),
0,
HTS_POS_MAX,
&r->ref_len[0]);
if (!r->ref[0]) {
r->ref[0] = NULL;
r->ref_id[0] = -1;
r->ref_len[0] = 0;
*ref = NULL;
return 0;
}
*ref = r->ref[0];
*ref_len = r->ref_len[0];
return 1;
}
// Initialise and destroy the base modifier state data. This is called
// as each new read is added or removed from the pileups.
static
int pileup_cd_create(void *data, const bam1_t *b, bam_pileup_cd *cd) {
int ret;
hts_base_mod_state *m = hts_base_mod_state_alloc();
ret = bam_parse_basemod(b, m);
cd->p = m;
return ret;
}
static
int pileup_cd_destroy(void *data, const bam1_t *b, bam_pileup_cd *cd) {
hts_base_mod_state_free(cd->p);
return 0;
}
static void
print_empty_pileup(FILE *fp, const mplp_conf_t *conf, const char *tname,
hts_pos_t pos, int n, const char *ref, hts_pos_t ref_len)
{
int i;
fprintf(fp, "%s\t%"PRIhts_pos"\t%c", tname, pos+1, (ref && pos < ref_len)? ref[pos] : 'N');
for (i = 0; i < n; ++i) {
fputs("\t0\t*\t*", fp);
int flag_value = MPLP_PRINT_MAPQ_CHAR;
while(flag_value < MPLP_PRINT_LAST) {
if (flag_value != MPLP_PRINT_MODS && (conf->flag & flag_value))
fputs("\t*", fp);
flag_value <<= 1;
}
if (conf->auxlist) {
int t = 0;
while(t++ < ((klist_t(auxlist) *)conf->auxlist)->size)
fputs("\t*", fp);
}
}
putc('\n', fp);
}
static int mplp_func(void *data, bam1_t *b)
{
char *ref;
mplp_aux_t *ma = (mplp_aux_t*)data;
int ret, skip = 0;
hts_pos_t ref_len;
do {
int has_ref;
ret = ma->iter? sam_itr_next(ma->fp, ma->iter, b) : sam_read1(ma->fp, ma->h, b);
if (ret < 0) break;
// The 'B' cigar operation is not part of the specification, considering as obsolete.
// bam_remove_B(b);
if (b->core.tid < 0 || (b->core.flag&BAM_FUNMAP)) { // exclude unmapped reads
skip = 1;
continue;
}
if (ma->conf->rflag_require && !(ma->conf->rflag_require&b->core.flag)) { skip = 1; continue; }
if (ma->conf->rflag_filter && ma->conf->rflag_filter&b->core.flag) { skip = 1; continue; }
if (ma->conf->bed && ma->conf->all == 0) { // test overlap
skip = !bed_overlap(ma->conf->bed, sam_hdr_tid2name(ma->h, b->core.tid), b->core.pos, bam_endpos(b));
if (skip) continue;
}
if (ma->conf->rghash) { // exclude read groups
uint8_t *rg = bam_aux_get(b, "RG");
skip = (rg && khash_str2int_get(ma->conf->rghash, (const char*)(rg+1), NULL)==0);
if (skip) continue;
}
if (ma->conf->flag & MPLP_ILLUMINA13) {
int i;
uint8_t *qual = bam_get_qual(b);
for (i = 0; i < b->core.l_qseq; ++i)
qual[i] = qual[i] > 31? qual[i] - 31 : 0;
}
if (ma->conf->fai && b->core.tid >= 0) {
has_ref = mplp_get_ref(ma, b->core.tid, &ref, &ref_len);
if (has_ref && ref_len <= b->core.pos) { // exclude reads outside of the reference sequence
fprintf(stderr,"[%s] Skipping because %"PRIhts_pos" is outside of %"PRIhts_pos" [ref:%d]\n",
__func__, (int64_t) b->core.pos, ref_len, b->core.tid);
skip = 1;
continue;
}
} else {
has_ref = 0;
}
skip = 0;
if (has_ref && (ma->conf->flag&MPLP_REALN)) sam_prob_realn(b, ref, ref_len, (ma->conf->flag & MPLP_REDO_BAQ)? 7 : 3);
if (has_ref && ma->conf->capQ_thres > 10) {
int q = sam_cap_mapq(b, ref, ref_len, ma->conf->capQ_thres);
if (q < 0) skip = 1;
else if (b->core.qual > q) b->core.qual = q;
}
if (b->core.qual < ma->conf->min_mq) skip = 1;
else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&BAM_FPAIRED) && !(b->core.flag&BAM_FPROPER_PAIR)) skip = 1;
} while (skip);
return ret;
}
static void group_smpl(mplp_pileup_t *m, bam_sample_t *sm, kstring_t *buf,
int n, char *const*fn, int *n_plp, const bam_pileup1_t **plp, int ignore_rg)
{
int i, j;
memset(m->n_plp, 0, m->n * sizeof(int));
for (i = 0; i < n; ++i) {
for (j = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = plp[i] + j;
uint8_t *q;
int id = -1;
q = ignore_rg? NULL : bam_aux_get(p->b, "RG");
if (q) id = bam_smpl_rg2smid(sm, fn[i], (char*)q+1, buf);
if (id < 0) id = bam_smpl_rg2smid(sm, fn[i], 0, buf);
if (id < 0 || id >= m->n) {
assert(q); // otherwise a bug
fprintf(stderr, "[%s] Read group %s used in file %s but absent from the header or an alignment missing read group.\n", __func__, (char*)q+1, fn[i]);
exit(EXIT_FAILURE);
}
if (m->n_plp[id] == m->m_plp[id]) {
m->m_plp[id] = m->m_plp[id]? m->m_plp[id]<<1 : 8;
m->plp[id] = realloc(m->plp[id], sizeof(bam_pileup1_t) * m->m_plp[id]);
}
m->plp[id][m->n_plp[id]++] = *p;
}
}
}
/*
* Performs pileup
* @param conf configuration for this pileup
* @param n number of files specified in fn
* @param fn filenames
* @param fn_idx index filenames
*/
static int mpileup(mplp_conf_t *conf, int n, char **fn, char **fn_idx)
{
extern void *bcf_call_add_rg(void *rghash, const char *hdtext, const char *list);
extern void bcf_call_del_rghash(void *rghash);
mplp_aux_t **data;
int i, tid, *n_plp, tid0 = 0, max_depth, max_indel_depth;
hts_pos_t pos, beg0 = 0, end0 = HTS_POS_MAX, ref_len;
const bam_pileup1_t **plp;
mplp_ref_t mp_ref = MPLP_REF_INIT;
bam_mplp_t iter;
sam_hdr_t *h = NULL; /* header of first file in input list */
char *ref;
void *rghash = NULL;
FILE *pileup_fp = NULL;
bcf_callaux_t *bca = NULL;
bcf_callret1_t *bcr = NULL;
bcf_call_t bc;
htsFile *bcf_fp = NULL;
bcf_hdr_t *bcf_hdr = NULL;
bam_sample_t *sm = NULL;
kstring_t buf;
mplp_pileup_t gplp;
memset(&gplp, 0, sizeof(mplp_pileup_t));
memset(&buf, 0, sizeof(kstring_t));
memset(&bc, 0, sizeof(bcf_call_t));
data = calloc(n, sizeof(mplp_aux_t*));
plp = calloc(n, sizeof(bam_pileup1_t*));
n_plp = calloc(n, sizeof(int));
sm = bam_smpl_init();
if (n == 0) {
fprintf(stderr,"[%s] no input file/data given\n", __func__);
exit(EXIT_FAILURE);
}
// read the header of each file in the list and initialize data
refs_t *refs = NULL;
for (i = 0; i < n; ++i) {
sam_hdr_t *h_tmp;
data[i] = calloc(1, sizeof(mplp_aux_t));
data[i]->fp = sam_open_format(fn[i], "rb", &conf->ga.in);
if ( !data[i]->fp )
{
fprintf(stderr, "[%s] failed to open %s: %s\n", __func__, fn[i], strerror(errno));
exit(EXIT_FAILURE);
}
if (hts_set_opt(data[i]->fp, CRAM_OPT_DECODE_MD, 0)) {
fprintf(stderr, "Failed to set CRAM_OPT_DECODE_MD value\n");
exit(EXIT_FAILURE);
}
if (!refs && conf->fai_fname) {
if (hts_set_fai_filename(data[i]->fp, conf->fai_fname) != 0) {
fprintf(stderr, "[%s] failed to process %s: %s\n",
__func__, conf->fai_fname, strerror(errno));
exit(EXIT_FAILURE);
}
refs = cram_get_refs(data[i]->fp);
} else if (conf->fai_fname) {
if (hts_set_opt(data[i]->fp, CRAM_OPT_SHARED_REF, refs) != 0) {
fprintf(stderr, "[%s] failed to process %s: %s\n",
__func__, conf->fai_fname, strerror(errno));
exit(EXIT_FAILURE);
}
}
data[i]->conf = conf;
data[i]->ref = &mp_ref;
h_tmp = sam_hdr_read(data[i]->fp);
if ( !h_tmp ) {
fprintf(stderr,"[%s] fail to read the header of %s\n", __func__, fn[i]);
exit(EXIT_FAILURE);
}
bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : sam_hdr_str(h_tmp));
if (conf->flag & MPLP_BCF) {
// Collect read group IDs with PL (platform) listed in pl_list (note: fragile, strstr search)
rghash = bcf_call_add_rg(rghash, sam_hdr_str(h_tmp), conf->pl_list);
}
if (conf->reg) {
hts_idx_t *idx = NULL;
// If index filename has not been specfied, look in BAM folder
if (fn_idx != NULL) {
idx = sam_index_load2(data[i]->fp, fn[i], fn_idx[i]);
} else {
idx = sam_index_load(data[i]->fp, fn[i]);
}
if (idx == NULL) {
fprintf(stderr, "[%s] fail to load index for %s\n", __func__, fn[i]);
exit(EXIT_FAILURE);
}
if ( (data[i]->iter=sam_itr_querys(idx, h_tmp, conf->reg)) == 0) {
fprintf(stderr, "[E::%s] fail to parse region '%s' with %s\n", __func__, conf->reg, fn[i]);
exit(EXIT_FAILURE);
}
if (i == 0) beg0 = data[i]->iter->beg, end0 = data[i]->iter->end, tid0 = data[i]->iter->tid;
hts_idx_destroy(idx);
}
else
data[i]->iter = NULL;
if (i == 0) h = data[i]->h = h_tmp; // save the header of the first file
else {
// FIXME: check consistency between h and h_tmp
sam_hdr_destroy(h_tmp);
// we store only the first file's header; it's (alleged to be)
// compatible with the i-th file's target_name lookup needs
data[i]->h = h;
}
}
fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n);
if (conf->flag & MPLP_BCF)
{
const char *mode;
// allocate data storage proportionate to number of samples being studied sm->n
gplp.n = sm->n;
gplp.n_plp = calloc(sm->n, sizeof(int));
gplp.m_plp = calloc(sm->n, sizeof(int));
gplp.plp = calloc(sm->n, sizeof(bam_pileup1_t*));
// write the VCF header
if ( conf->flag & MPLP_VCF )
mode = (conf->flag&MPLP_NO_COMP)? "wu" : "wz"; // uncompressed VCF or compressed VCF
else
mode = (conf->flag&MPLP_NO_COMP)? "wub" : "wb"; // uncompressed BCF or compressed BCF
bcf_fp = bcf_open(conf->output_fname? conf->output_fname : "-", mode);
if (bcf_fp == NULL) {
fprintf(stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname? conf->output_fname : "standard output", strerror(errno));
exit(EXIT_FAILURE);
}
autoflush_if_stdout(bcf_fp, conf->output_fname);
// BCF header creation
bcf_hdr = bcf_hdr_init("w");
kstring_t str = {0,0,NULL};
ksprintf(&str, "##samtoolsVersion=%s+htslib-%s\n",samtools_version(),hts_version());
bcf_hdr_append(bcf_hdr, str.s);
str.l = 0;
ksprintf(&str, "##samtoolsCommand=samtools mpileup");
for (i=1; i<conf->argc; i++) ksprintf(&str, " %s", conf->argv[i]);
kputc('\n', &str);
bcf_hdr_append(bcf_hdr, str.s);
if (conf->fai_fname)
{
str.l = 0;
ksprintf(&str, "##reference=file://%s\n", conf->fai_fname);
bcf_hdr_append(bcf_hdr, str.s);
}
// Translate BAM @SQ tags to BCF ##contig tags
// todo: use/write new BAM header manipulation routines, fill also UR, M5
for (i=0; i < sam_hdr_nref(h); i++)
{
str.l = 0;
ksprintf(&str, "##contig=<ID=%s,length=%"PRId64">", sam_hdr_tid2name(h, i), (int64_t) sam_hdr_tid2len(h, i));
bcf_hdr_append(bcf_hdr, str.s);
}
free(str.s);
bcf_hdr_append(bcf_hdr,"##ALT=<ID=*,Description=\"Represents allele(s) other than observed.\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=IDV,Number=1,Type=Integer,Description=\"Maximum number of reads supporting an indel\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=IMF,Number=1,Type=Float,Description=\"Maximum fraction of reads supporting an indel\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)\",Version=\"3\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=RPB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias (bigger is better)\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias (bigger is better)\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=BQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias (bigger is better)\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQSB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)\">");
#if CDF_MWU_TESTS
bcf_hdr_append(bcf_hdr,"##INFO=<ID=RPB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias [CDF] (bigger is better)\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias [CDF] (bigger is better)\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=BQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias [CDF] (bigger is better)\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQSB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias [CDF] (bigger is better)\">");
#endif
bcf_hdr_append(bcf_hdr,"##INFO=<ID=SGB,Number=1,Type=Float,Description=\"Segregation based metric.\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQ0F,Number=1,Type=Float,Description=\"Fraction of MQ0 reads (smaller is better)\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=I16,Number=16,Type=Float,Description=\"Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=QS,Number=R,Type=Float,Description=\"Auxiliary tag used for calling\">");
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">");
if ( conf->fmt_flag&B2B_FMT_DP )
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Number of high-quality bases\">");
if ( conf->fmt_flag&B2B_FMT_DV )
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"Number of high-quality non-reference bases\">");
if ( conf->fmt_flag&B2B_FMT_DPR )
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
if ( conf->fmt_flag&B2B_INFO_DPR )
bcf_hdr_append(bcf_hdr,"##INFO=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
if ( conf->fmt_flag&B2B_FMT_DP4 )
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases\">");
if ( conf->fmt_flag&B2B_FMT_SP )
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">");
if ( conf->fmt_flag&B2B_FMT_AD )
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths\">");
if ( conf->fmt_flag&B2B_FMT_ADF )
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=ADF,Number=R,Type=Integer,Description=\"Allelic depths on the forward strand\">");
if ( conf->fmt_flag&B2B_FMT_ADR )
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=ADR,Number=R,Type=Integer,Description=\"Allelic depths on the reverse strand\">");
if ( conf->fmt_flag&B2B_INFO_AD )
bcf_hdr_append(bcf_hdr,"##INFO=<ID=AD,Number=R,Type=Integer,Description=\"Total allelic depths\">");
if ( conf->fmt_flag&B2B_INFO_ADF )
bcf_hdr_append(bcf_hdr,"##INFO=<ID=ADF,Number=R,Type=Integer,Description=\"Total allelic depths on the forward strand\">");
if ( conf->fmt_flag&B2B_INFO_ADR )
bcf_hdr_append(bcf_hdr,"##INFO=<ID=ADR,Number=R,Type=Integer,Description=\"Total allelic depths on the reverse strand\">");
for (i=0; i<sm->n; i++)
bcf_hdr_add_sample(bcf_hdr, sm->smpl[i]);
bcf_hdr_add_sample(bcf_hdr, NULL);
if (bcf_hdr_write(bcf_fp, bcf_hdr) != 0) {
print_error_errno("mpileup", "Failed to write VCF/BCF header to \"%s\"",
conf->output_fname? conf->output_fname : "standard output");
exit(EXIT_FAILURE);
}
// End of BCF header creation
// Initialise the calling algorithm
bca = bcf_call_init(-1., conf->min_baseQ);
bcr = calloc(sm->n, sizeof(bcf_callret1_t));
bca->rghash = rghash;
bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ;
bca->min_frac = conf->min_frac;
bca->min_support = conf->min_support;
bca->per_sample_flt = conf->flag & MPLP_PER_SAMPLE;
bc.bcf_hdr = bcf_hdr;
bc.n = sm->n;
bc.PL = malloc(15 * sm->n * sizeof(*bc.PL));
if (conf->fmt_flag)
{
assert( sizeof(float)==sizeof(int32_t) );
bc.DP4 = malloc(sm->n * sizeof(int32_t) * 4);
bc.fmt_arr = malloc(sm->n * sizeof(float)); // all fmt_flag fields
if ( conf->fmt_flag&(B2B_INFO_DPR|B2B_FMT_DPR|B2B_INFO_AD|B2B_INFO_ADF|B2B_INFO_ADR|B2B_FMT_AD|B2B_FMT_ADF|B2B_FMT_ADR) )
{
// first B2B_MAX_ALLELES fields for total numbers, the rest per-sample
bc.ADR = (int32_t*) malloc((sm->n+1)*B2B_MAX_ALLELES*sizeof(int32_t));
bc.ADF = (int32_t*) malloc((sm->n+1)*B2B_MAX_ALLELES*sizeof(int32_t));
for (i=0; i<sm->n; i++)
{
bcr[i].ADR = bc.ADR + (i+1)*B2B_MAX_ALLELES;
bcr[i].ADF = bc.ADF + (i+1)*B2B_MAX_ALLELES;
}
}
}
}
else {
pileup_fp = conf->output_fname? fopen(conf->output_fname, "w") : stdout;
if (pileup_fp == NULL) {
fprintf(stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname, strerror(errno));
exit(EXIT_FAILURE);
}
}
// init pileup
iter = bam_mplp_init(n, mplp_func, (void**)data);
if (conf->flag & MPLP_PRINT_MODS) {
bam_mplp_constructor(iter, pileup_cd_create);
bam_mplp_destructor(iter, pileup_cd_destroy);
}
if ( conf->flag & MPLP_SMART_OVERLAPS ) bam_mplp_init_overlaps(iter);
if ( !conf->max_depth ) {
max_depth = INT_MAX;
fprintf(stderr, "[%s] Max depth set to maximum value (%d)\n", __func__, INT_MAX);
} else {
max_depth = conf->max_depth;
if ( max_depth * n > 1<<20 )
fprintf(stderr, "[%s] Combined max depth is above 1M. Potential memory hog!\n", __func__);
}
// Only used when writing BCF
max_indel_depth = conf->max_indel_depth * sm->n;
bam_mplp_set_maxcnt(iter, max_depth);
bcf1_t *bcf_rec = bcf_init1();
int ret;
int last_tid = -1;
hts_pos_t last_pos = -1;
// begin pileup
while ( (ret=bam_mplp64_auto(iter, &tid, &pos, n_plp, plp)) > 0) {
if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested
mplp_get_ref(data[0], tid, &ref, &ref_len);
//printf("tid=%d len=%d ref=%p/%s\n", tid, ref_len, ref, ref);
if (conf->flag & MPLP_BCF) {
int total_depth, _ref0, ref16;
if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, sam_hdr_tid2name(h, tid), pos, pos+1)) continue;
for (i = total_depth = 0; i < n; ++i) total_depth += n_plp[i];
group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp, conf->flag & MPLP_IGNORE_RG);
_ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
ref16 = seq_nt16_table[_ref0];
bcf_callaux_clean(bca, &bc);
for (i = 0; i < gplp.n; ++i)
bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
bc.tid = tid; bc.pos = pos;
bcf_call_combine(gplp.n, bcr, bca, ref16, &bc);
bcf_clear1(bcf_rec);
bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, 0, 0);
if (bcf_write1(bcf_fp, bcf_hdr, bcf_rec) != 0) {
print_error_errno("mpileup", "Failed to write VCF/BCF record to \"%s\"",
conf->output_fname?conf->output_fname:"standard output");
exit(EXIT_FAILURE);
}
// call indels; todo: subsampling with total_depth>max_indel_depth instead of ignoring?
if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0)
{
bcf_callaux_clean(bca, &bc);
for (i = 0; i < gplp.n; ++i)
bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i);
if (bcf_call_combine(gplp.n, bcr, bca, -1, &bc) >= 0) {
bcf_clear1(bcf_rec);
bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, bca, ref);
if (bcf_write1(bcf_fp, bcf_hdr, bcf_rec) != 0) {
print_error_errno("mpileup", "Failed to write VCF/BCF record to \"%s\"",
conf->output_fname?conf->output_fname:"standard output");
exit(EXIT_FAILURE);
}
}
}
} else {
if (conf->all) {
// Deal with missing portions of previous tids
while (tid > last_tid) {
if (last_tid >= 0 && !conf->reg) {
while (++last_pos < sam_hdr_tid2len(h, last_tid)) {
if (conf->bed && bed_overlap(conf->bed, sam_hdr_tid2name(h, last_tid), last_pos, last_pos + 1) == 0)
continue;
print_empty_pileup(pileup_fp, conf, sam_hdr_tid2name(h, last_tid), last_pos, n, ref, ref_len);
}
}
last_tid++;
last_pos = -1;
if (conf->all < 2)
break;
}
}
if (conf->all) {
// Deal with missing portion of current tid
while (++last_pos < pos) {
if (conf->reg && last_pos < beg0) continue; // out of range; skip
if (conf->bed && bed_overlap(conf->bed, sam_hdr_tid2name(h, tid), last_pos, last_pos + 1) == 0)
continue;
print_empty_pileup(pileup_fp, conf, sam_hdr_tid2name(h, tid), last_pos, n, ref, ref_len);
}
last_tid = tid;
last_pos = pos;
}
if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, sam_hdr_tid2name(h, tid), pos, pos+1)) continue;
fprintf(pileup_fp, "%s\t%"PRIhts_pos"\t%c", sam_hdr_tid2name(h, tid), pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
for (i = 0; i < n; ++i) {
int j, cnt;
for (j = cnt = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = plp[i] + j;
int c = p->qpos < p->b->core.l_qseq
? bam_get_qual(p->b)[p->qpos]
: 0;
if (c >= conf->min_baseQ) ++cnt;
}
fprintf(pileup_fp, "\t%d\t", cnt);
if (n_plp[i] == 0) {
fputs("*\t*", pileup_fp);
int flag_value = MPLP_PRINT_MAPQ_CHAR;
while(flag_value < MPLP_PRINT_LAST) {
if (flag_value != MPLP_PRINT_MODS
&& (conf->flag & flag_value))
fputs("\t*", pileup_fp);
flag_value <<= 1;
}
if (conf->auxlist) {
int t = 0;
while(t++ < ((klist_t(auxlist) *)conf->auxlist)->size)
fputs("\t*", pileup_fp);
}
} else {
int n = 0;
kstring_t ks = KS_INITIALIZE;
for (j = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = plp[i] + j;
int c = p->qpos < p->b->core.l_qseq
? bam_get_qual(p->b)[p->qpos]
: 0;
if (c >= conf->min_baseQ) {
n++;
if (pileup_seq(pileup_fp, plp[i] + j, pos, ref_len,
ref, &ks, conf->rev_del,
conf->no_ins, conf->no_ins_mods,
conf->no_del, conf->no_ends) < 0) {
ret = 1;
goto fail;
}
}
}
if (!n) putc('*', pileup_fp);
/* Print base qualities */
n = 0;
ks_free(&ks);
putc('\t', pileup_fp);
for (j = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = plp[i] + j;
int c = p->qpos < p->b->core.l_qseq
? bam_get_qual(p->b)[p->qpos]
: 0;
if (c >= conf->min_baseQ) {
c = c + 33 < 126? c + 33 : 126;
putc(c, pileup_fp);
n++;
}
}
if (!n) putc('*', pileup_fp);
/* Print selected columns */
int flag_value = MPLP_PRINT_MAPQ_CHAR;
while(flag_value < MPLP_PRINT_LAST) {
if (flag_value != MPLP_PRINT_MODS
&& (conf->flag & flag_value)) {
n = 0;
putc('\t', pileup_fp);
for (j = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = &plp[i][j];
int c = p->qpos < p->b->core.l_qseq
? bam_get_qual(p->b)[p->qpos]
: 0;
if ( c < conf->min_baseQ ) continue;
if (n > 0 && flag_value != MPLP_PRINT_MAPQ_CHAR) putc(',', pileup_fp);
n++;
switch (flag_value) {
case MPLP_PRINT_MAPQ_CHAR:
c = p->b->core.qual + 33;
if (c > 126) c = 126;
putc(c, pileup_fp);
break;
case MPLP_PRINT_QPOS:
// query position in current orientation
fprintf(pileup_fp, "%d", p->qpos + 1);
break;
case MPLP_PRINT_QPOS5: {
// query position in 5' to 3' orientation
int pos5 = bam_is_rev(p->b)
? p->b->core.l_qseq-p->qpos + p->is_del
: p->qpos + 1;
fprintf(pileup_fp, "%d", pos5);
break;
}
case MPLP_PRINT_QNAME:
fputs(bam_get_qname(p->b), pileup_fp);
break;
case MPLP_PRINT_FLAG:
fprintf(pileup_fp, "%d", p->b->core.flag);
break;
case MPLP_PRINT_RNAME:
if (p->b->core.tid >= 0)
fputs(sam_hdr_tid2name(h, p->b->core.tid), pileup_fp);
else
putc('*', pileup_fp);
break;
case MPLP_PRINT_POS:
fprintf(pileup_fp, "%"PRId64, (int64_t) p->b->core.pos + 1);
break;
case MPLP_PRINT_MAPQ:
fprintf(pileup_fp, "%d", p->b->core.qual);
break;
case MPLP_PRINT_RNEXT:
if (p->b->core.mtid >= 0)
fputs(sam_hdr_tid2name(h, p->b->core.mtid), pileup_fp);
else
putc('*', pileup_fp);
break;
case MPLP_PRINT_PNEXT:
fprintf(pileup_fp, "%"PRId64, (int64_t) p->b->core.mpos + 1);
break;
}
}
if (!n) putc('*', pileup_fp);
}
flag_value <<= 1;
}
/* Print selected tags */
klist_t(auxlist) *auxlist_p = ((klist_t(auxlist) *)conf->auxlist);
if (auxlist_p && auxlist_p->size) {
kliter_t(auxlist) *aux;
for (aux = kl_begin(auxlist_p); aux != kl_end(auxlist_p); aux = kl_next(aux)) {
n = 0;
putc('\t', pileup_fp);
for (j = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = &plp[i][j];
int c = p->qpos < p->b->core.l_qseq
? bam_get_qual(p->b)[p->qpos]
: 0;
if ( c < conf->min_baseQ ) continue;
if (n > 0) putc(conf->sep, pileup_fp);
n++;
uint8_t* tag_u = bam_aux_get(p->b, kl_val(aux));
if (!tag_u) {
putc(conf->empty , pileup_fp);
continue;
}
/* Tag value is string */
if (*tag_u == 'Z' || *tag_u == 'H') {
char *tag_s = bam_aux2Z(tag_u);
if (!tag_s) continue;
fputs(tag_s, pileup_fp);
}
/* Tag value is integer */
if (*tag_u == 'I' || *tag_u == 'i' || *tag_u == 'C' || *tag_u == 'c' || *tag_u == 'S' || *tag_u == 's') {
int64_t tag_i = bam_aux2i(tag_u);
fprintf(pileup_fp, "%" PRId64 "", tag_i);
}
/* Tag value is float */
if (*tag_u == 'd' || *tag_u == 'f') {
double tag_f = bam_aux2f(tag_u);