-
Notifications
You must be signed in to change notification settings - Fork 240
/
vcfcall.c
1206 lines (1101 loc) · 48.4 KB
/
vcfcall.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
/* vcfcall.c -- SNP/indel variant calling from VCF/BCF.
Copyright (C) 2013-2024 Genome Research Ltd.
Author: Petr Danecek <[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 <stdarg.h>
#include <string.h>
#include <strings.h>
#include <assert.h>
#include <errno.h>
#include <unistd.h>
#include <getopt.h>
#include <math.h>
#include <htslib/vcf.h>
#include <time.h>
#include <stdarg.h>
#include <htslib/kfunc.h>
#include <htslib/synced_bcf_reader.h>
#include <htslib/khash_str2int.h>
#include <ctype.h>
#include "bcftools.h"
#include "call.h"
#include "prob1.h"
#include "ploidy.h"
#include "gvcf.h"
#include "regidx.h"
#include "vcfbuf.h"
void error(const char *format, ...);
#define CF_NO_GENO 1
#define CF_INS_MISSED (1<<1)
#define CF_CCALL (1<<2)
// (1<<3)
// (1<<4)
// (1<<5)
#define CF_ACGT_ONLY (1<<6)
#define CF_QCALL (1<<7)
#define CF_ADJLD (1<<8)
#define CF_NO_INDEL (1<<9)
#define CF_ANNO_MAX (1<<10)
#define CF_MCALL (1<<11)
#define CF_PAIRCALL (1<<12)
#define CF_QCNT (1<<13)
#define CF_INDEL_ONLY (1<<14)
typedef struct
{
tgt_als_t *als;
int nmatch_als, ibuf;
}
rec_tgt_t;
typedef struct
{
int flag; // combination of CF_* flags above
int output_type, n_threads, record_cmd_line, clevel;
htsFile *bcf_in, *out_fh;
char *bcf_fname, *output_fname;
char **samples; // for subsampling and ploidy
int nsamples, *samples_map; // mapping from output sample names to original VCF
char *regions, *targets; // regions to process
int regions_is_file, targets_is_file, regions_overlap;
regidx_t *tgt_idx;
regitr_t *tgt_itr, *tgt_itr_prev, *tgt_itr_tmp;
vcfbuf_t *vcfbuf;
char *samples_fname;
int samples_is_file;
int *sample2sex; // mapping for ploidy. If negative, interpreted as -1*ploidy
int *sex2ploidy, *sex2ploidy_prev, nsex;
ploidy_t *ploidy;
gvcf_t *gvcf;
bcf1_t *missed_line;
call_t aux; // parameters and temporary data
kstring_t str;
int argc;
char **argv;
char *index_fn;
int write_index;
// int flag, prior_type, n1, n_sub, *sublist, n_perm;
// uint32_t *trio_aux;
// char *prior_file, **subsam;
// uint8_t *ploidy;
// double theta, pref, indel_frac, min_smpl_frac, min_lrt;
// Permutation tests
// int n_perm, *seeds;
// double min_perm_p;
// void *bed;
}
args_t;
static char **add_sample(void *name2idx, char **lines, int *nlines, int *mlines, char *name, char sex, int *ith)
{
int ret = khash_str2int_get(name2idx, name, ith);
if ( ret==0 ) return lines;
hts_expand(char*,(*nlines+1),*mlines,lines);
int len = strlen(name);
lines[*nlines] = (char*) malloc(len+3);
memcpy(lines[*nlines],name,len);
lines[*nlines][len] = ' ';
lines[*nlines][len+1] = sex;
lines[*nlines][len+2] = 0;
*ith = *nlines;
(*nlines)++;
khash_str2int_set(name2idx, strdup(name), *ith);
return lines;
}
typedef struct
{
const char *alias, *about, *ploidy;
}
ploidy_predef_t;
static ploidy_predef_t ploidy_predefs[] =
{
{ .alias = "GRCh37",
.about = "Human Genome reference assembly GRCh37 / hg19",
.ploidy =
"X 1 60000 M 1\n"
"X 2699521 154931043 M 1\n"
"Y 1 59373566 M 1\n"
"Y 1 59373566 F 0\n"
"MT 1 16569 M 1\n"
"MT 1 16569 F 1\n"
"chrX 1 60000 M 1\n"
"chrX 2699521 154931043 M 1\n"
"chrY 1 59373566 M 1\n"
"chrY 1 59373566 F 0\n"
"chrM 1 16569 M 1\n"
"chrM 1 16569 F 1\n"
"* * * M 2\n"
"* * * F 2\n"
},
{ .alias = "GRCh38",
.about = "Human Genome reference assembly GRCh38 / hg38",
.ploidy =
"X 1 9999 M 1\n"
"X 2781480 155701381 M 1\n"
"Y 1 57227415 M 1\n"
"Y 1 57227415 F 0\n"
"MT 1 16569 M 1\n"
"MT 1 16569 F 1\n"
"chrX 1 9999 M 1\n"
"chrX 2781480 155701381 M 1\n"
"chrY 1 57227415 M 1\n"
"chrY 1 57227415 F 0\n"
"chrM 1 16569 M 1\n"
"chrM 1 16569 F 1\n"
"* * * M 2\n"
"* * * F 2\n"
},
{ .alias = "X",
.about = "Treat male samples as haploid and female as diploid regardless of the chromosome name",
.ploidy =
"* * * M 1\n"
"* * * F 2\n"
},
{ .alias = "Y",
.about = "Treat male samples as haploid and female as no-copy, regardless of the chromosome name",
.ploidy =
"* * * M 1\n"
"* * * F 0\n"
},
{ .alias = "1",
.about = "Treat all samples as haploid",
.ploidy =
"* * * * 1\n"
},
{ .alias = "2",
.about = "Treat all samples as diploid",
.ploidy =
"* * * * 2\n"
},
{
.alias = NULL,
.about = NULL,
.ploidy = NULL,
}
};
// only 5 columns are required and the first is ignored:
// ignored,sample,father(or 0),mother(or 0),sex(1=M,2=F)
static char **parse_ped_samples(call_t *call, char **vals, int nvals, int *nsmpl)
{
int i, j, mlines = 0, nlines = 0;
kstring_t str = {0,0,0}, fam_str = {0,0,0};
void *name2idx = khash_str2int_init();
char **lines = NULL;
for (i=0; i<nvals; i++)
{
str.l = 0;
kputs(vals[i], &str);
char *col_ends[5], *tmp = str.s;
j = 0;
while ( *tmp && j<5 )
{
if ( isspace(*tmp) )
{
*tmp = 0;
++tmp;
while ( isspace(*tmp) ) tmp++; // allow multiple spaces
col_ends[j] = tmp-1;
j++;
continue;
}
tmp++;
}
if ( j<4 ) break;
char sex;
if ( col_ends[3][1]=='1' ) sex = 'M';
else if ( col_ends[3][1]=='2' ) sex = 'F';
else break;
lines = add_sample(name2idx, lines, &nlines, &mlines, col_ends[0]+1, sex, &j);
if ( strcmp(col_ends[1]+1,"0") && strcmp(col_ends[2]+1,"0") ) // father and mother
{
call->nfams++;
hts_expand(family_t, call->nfams, call->mfams, call->fams);
family_t *fam = &call->fams[call->nfams-1];
fam_str.l = 0;
ksprintf(&fam_str,"father=%s, mother=%s, child=%s", col_ends[1]+1,col_ends[2]+1,col_ends[0]+1);
fam->name = strdup(fam_str.s);
if ( !khash_str2int_has_key(name2idx, col_ends[1]+1) )
lines = add_sample(name2idx, lines, &nlines, &mlines, col_ends[1]+1, 'M', &fam->sample[FATHER]);
if ( !khash_str2int_has_key(name2idx, col_ends[2]+1) )
lines = add_sample(name2idx, lines, &nlines, &mlines, col_ends[2]+1, 'F', &fam->sample[MOTHER]);
khash_str2int_get(name2idx, col_ends[0]+1, &fam->sample[CHILD]);
khash_str2int_get(name2idx, col_ends[1]+1, &fam->sample[FATHER]);
khash_str2int_get(name2idx, col_ends[2]+1, &fam->sample[MOTHER]);
}
}
free(str.s);
free(fam_str.s);
khash_str2int_destroy_free(name2idx);
if ( i!=nvals ) return NULL; // not a ped file
*nsmpl = nlines;
return lines;
}
/*
* Reads sample names and their ploidy (optional) from a file.
* Alternatively, if no such file exists, the file name is interpreted
* as a comma-separated list of samples. When ploidy is not present,
* the default ploidy 2 is assumed.
*/
static void set_samples(args_t *args, const char *fn, int is_file)
{
int i, nlines;
char **lines = hts_readlist(fn, is_file, &nlines);
if ( !lines ) error("Could not read the file: %s\n", fn);
int nsmpls;
char **smpls = parse_ped_samples(&args->aux, lines, nlines, &nsmpls);
if ( smpls )
{
for (i=0; i<nlines; i++) free(lines[i]);
free(lines);
lines = smpls;
nlines = nsmpls;
}
else if ( is_file )
fprintf(stderr,"Note: could not parse as PED: %s\n",fn);
args->samples_map = (int*) malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr)); // for subsetting
args->sample2sex = (int*) malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr));
int dflt_sex_id = ploidy_nsex(args->ploidy) - 1;
for (i=0; i<bcf_hdr_nsamples(args->aux.hdr); i++) args->sample2sex[i] = dflt_sex_id;
int *old2new = (int*) malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr));
for (i=0; i<bcf_hdr_nsamples(args->aux.hdr); i++) old2new[i] = -1;
int nsmpl = 0, map_needed = 0;
for (i=0; i<nlines; i++)
{
char *ss = lines[i];
while ( *ss && isspace(*ss) ) ss++;
if ( !*ss ) error("Could not parse: %s\n", lines[i]);
if ( *ss=='#' ) continue;
char *se = ss;
while ( *se && !isspace(*se) ) se++;
char x = *se, *xptr = se; *se = 0;
int ismpl = bcf_hdr_id2int(args->aux.hdr, BCF_DT_SAMPLE, ss);
if ( ismpl < 0 ) { fprintf(stderr,"Warning: No such sample in the VCF: %s\n",ss); continue; }
if ( old2new[ismpl] != -1 ) { fprintf(stderr,"Warning: The sample is listed multiple times: %s\n",ss); continue; }
ss = se+(x != '\0');
while ( *ss && isspace(*ss) ) ss++;
if ( !*ss ) ss = "2"; // default ploidy
se = ss;
while ( *se && !isspace(*se) ) se++;
if ( se==ss ) { *xptr = x; error("Could not parse: \"%s\"\n", lines[i]); }
if ( ss[1]==0 && (ss[0]=='0' || ss[0]=='1' || ss[0]=='2') )
args->sample2sex[nsmpl] = -1*(ss[0]-'0');
else
args->sample2sex[nsmpl] = ploidy_add_sex(args->ploidy, ss);
if ( ismpl!=nsmpl ) map_needed = 1;
args->samples_map[nsmpl] = ismpl;
old2new[ismpl] = nsmpl;
nsmpl++;
}
for (i=0; i<args->aux.nfams; i++)
{
int j, nmiss = 0;
family_t *fam = &args->aux.fams[i];
for (j=0; j<3; j++)
{
fam->sample[i] = old2new[fam->sample[i]];
if ( fam->sample[i]<0 ) nmiss++;
}
assert( nmiss==0 || nmiss==3 );
}
free(old2new);
if ( !map_needed ) { free(args->samples_map); args->samples_map = NULL; }
args->nsamples = nsmpl;
args->samples = lines;
}
static void init_missed_line(args_t *args)
{
int i;
for (i=0; i<bcf_hdr_nsamples(args->aux.hdr); i++)
{
args->aux.gts[i*2] = bcf_gt_missing;
args->aux.gts[i*2+1] = bcf_int32_vector_end;
}
args->missed_line = bcf_init1();
bcf_update_genotypes(args->aux.hdr, args->missed_line, args->aux.gts, 2*bcf_hdr_nsamples(args->aux.hdr));
bcf_float_set_missing(args->missed_line->qual);
}
static int tgt_parse(const char *line, char **chr_beg, char **chr_end, uint32_t *beg, uint32_t *end, void *payload, void *usr)
{
char *ss = (char*) line;
while ( *ss && isspace(*ss) ) ss++;
if ( !*ss ) { fprintf(stderr,"Could not parse the line: %s\n", line); return -2; }
if ( *ss=='#' ) return -1; // skip comments
char *se = ss;
while ( *se && !isspace(*se) ) se++;
*chr_beg = ss;
*chr_end = se-1;
if ( !*se ) { fprintf(stderr,"Could not parse the line: %s\n", line); return -2; }
ss = se+1;
*beg = strtod(ss, &se);
if ( ss==se ) { fprintf(stderr,"Could not parse tab line: %s\n", line); return -2; }
if ( *beg==0 ) { fprintf(stderr,"Could not parse tab line, expected 1-based coordinate: %s\n", line); return -2; }
(*beg)--;
*end = *beg;
if ( !usr ) return 0; // allele information not required
ss = se+1;
tgt_als_t *als = (tgt_als_t*)payload;
als->used = 0;
als->n = 0;
als->allele = NULL;
while ( *ss )
{
se = ss;
while ( *se && *se!=',' && !isspace(*se) ) se++;
als->n++;
als->allele = (char**)realloc(als->allele,als->n*sizeof(*als->allele));
als->allele[als->n-1] = (char*)malloc(se-ss+1);
memcpy(als->allele[als->n-1],ss,se-ss);
als->allele[als->n-1][se-ss] = 0;
ss = se+1;
if ( !*se || isspace(*se) ) break;
}
if ( als->n<2 ) error("Unable to parse the -T file; expected CHROM\\tPOS\\tREF,ALT with -C alleles but found instead:\n\t%s\n",line);
return 0;
}
static void tgt_free(void *payload)
{
tgt_als_t *als = (tgt_als_t*)payload;
int i;
for (i=0; i<als->n; i++) free(als->allele[i]);
free(als->allele);
}
static void tgt_flush_region(args_t *args, char *chr, uint32_t beg, uint32_t end)
{
if ( !regidx_overlap(args->tgt_idx, chr,beg,end,args->tgt_itr_tmp) ) return;
while ( regitr_overlap(args->tgt_itr_tmp) )
{
if ( args->tgt_itr_tmp->beg < beg ) continue;
tgt_als_t *tgt_als = ®itr_payload(args->tgt_itr_tmp,tgt_als_t);
if ( tgt_als->used ) continue;
args->missed_line->rid = bcf_hdr_name2id(args->aux.hdr,chr);
args->missed_line->pos = args->tgt_itr_tmp->beg;
bcf_unpack(args->missed_line,BCF_UN_ALL);
bcf_update_alleles(args->aux.hdr, args->missed_line, (const char**)tgt_als->allele, tgt_als->n);
tgt_als->used = 1;
if ( bcf_write1(args->out_fh, args->aux.hdr, args->missed_line)!=0 ) error("[%s] Error: failed to write to %s\n", __func__,args->output_fname);
}
}
static void tgt_flush(args_t *args, bcf1_t *rec)
{
if ( rec )
{
char *chr = (char*)bcf_seqname(args->aux.hdr,rec);
if ( !args->tgt_itr_prev ) // first record
tgt_flush_region(args,chr,0,rec->pos-1);
else if ( strcmp(chr,args->tgt_itr_prev->seq) ) // first record on a new chromosome
{
tgt_flush_region(args,args->tgt_itr_prev->seq,args->tgt_itr_prev->beg+1,REGIDX_MAX);
tgt_flush_region(args,chr,0,rec->pos-1);
}
else // another record on the same chromosome
tgt_flush_region(args,args->tgt_itr_prev->seq,args->tgt_itr_prev->beg,rec->pos-1);
}
else
{
// flush everything
if ( args->tgt_itr_prev )
tgt_flush_region(args,args->tgt_itr_prev->seq,args->tgt_itr_prev->beg,REGIDX_MAX);
int i, nchr = 0;
char **chr = regidx_seq_names(args->tgt_idx, &nchr);
for (i=0; i<nchr; i++)
tgt_flush_region(args,chr[i],0,REGIDX_MAX);
}
}
inline static int is_indel(int nals, char **als)
{
// This is mpileup output, we can make some assumption:
// - no MNPs
// - "<*>" is not present at indels sites and there are no other symbolic alleles than <*>
if ( als[1][0]=='<' ) return 0;
int i;
for (i=0; i<nals; i++)
{
if ( als[i][0]=='<' ) continue;
if ( als[i][1] ) return 1;
}
return 0;
}
bcf1_t *next_line(args_t *args)
{
bcf1_t *rec = NULL;
if ( !args->vcfbuf )
{
while ( bcf_sr_next_line(args->aux.srs) )
{
rec = args->aux.srs->readers[0].buffer[0];
if ( args->aux.srs->errnum || rec->errcode ) error("Error: could not parse the input VCF\n");
if ( args->tgt_idx )
{
if ( !regidx_overlap(args->tgt_idx, bcf_seqname(args->aux.hdr,rec),rec->pos,rec->pos,args->tgt_itr) ) continue;
// For backward compatibility: require the exact position, not an interval overlap
int pos_match = 0;
while ( regitr_overlap(args->tgt_itr) )
{
if ( args->tgt_itr->beg != rec->pos ) continue;
pos_match = 1;
break;
}
if ( !pos_match ) continue;
}
if ( args->samples_map ) bcf_subset(args->aux.hdr, rec, args->nsamples, args->samples_map);
bcf_unpack(rec, BCF_UN_STR);
return rec;
}
return NULL;
}
// If we are here,-C alleles was given and vcfbuf and tgt_idx are set
// Fill the buffer with duplicate lines
int vcfbuf_full = 1;
int nbuf = vcfbuf_nsites(args->vcfbuf);
bcf1_t *rec0 = NULL, *recN = NULL;
if ( nbuf==0 ) vcfbuf_full = 0;
else if ( nbuf==1 )
{
vcfbuf_full = 0;
rec0 = vcfbuf_peek(args->vcfbuf, 0);
}
else
{
rec0 = vcfbuf_peek(args->vcfbuf, 0);
recN = vcfbuf_peek(args->vcfbuf, nbuf-1);
if ( rec0->rid == recN->rid && rec0->pos == recN->pos ) vcfbuf_full = 0;
}
if ( !vcfbuf_full )
{
while ( bcf_sr_next_line(args->aux.srs) )
{
rec = args->aux.srs->readers[0].buffer[0];
if ( args->aux.srs->errnum || rec->errcode ) error("Error: could not parse the input VCF\n");
if ( !regidx_overlap(args->tgt_idx, bcf_seqname(args->aux.hdr,rec),rec->pos,rec->pos,args->tgt_itr) ) continue;
// as above: require the exact position, not an interval overlap
int exact_match = 0;
while ( regitr_overlap(args->tgt_itr) )
{
if ( args->tgt_itr->beg != rec->pos ) continue;
exact_match = 1;
break;
}
if ( !exact_match ) continue;
if ( args->samples_map ) bcf_subset(args->aux.hdr, rec, args->nsamples, args->samples_map);
bcf_unpack(rec, BCF_UN_STR);
if ( !rec0 ) rec0 = rec;
recN = rec;
args->aux.srs->readers[0].buffer[0] = vcfbuf_push(args->vcfbuf, rec);
if ( rec0->rid!=recN->rid || rec0->pos!=recN->pos ) break;
}
}
nbuf = vcfbuf_nsites(args->vcfbuf);
int n, i,j;
for (n=nbuf; n>1; n--)
{
recN = vcfbuf_peek(args->vcfbuf, n-1);
if ( rec0->rid==recN->rid && rec0->pos==recN->pos ) break;
}
if ( n==0 )
{
assert( !nbuf );
return NULL;
}
// Find the VCF and tab record with the best matching combination of alleles, prioritize
// records of the same type (snp vs indel)
rec_tgt_t rec_tgt;
memset(&rec_tgt,0,sizeof(rec_tgt));
regidx_overlap(args->tgt_idx, bcf_seqname(args->aux.hdr,rec0),rec0->pos,rec0->pos,args->tgt_itr);
regitr_t *tmp_itr = regitr_init(args->tgt_idx);
for (i=0; i<n; i++)
{
regitr_copy(tmp_itr, args->tgt_itr);
rec = vcfbuf_peek(args->vcfbuf, i);
int rec_indel = is_indel(rec->n_allele, rec->d.allele) ? 1 : -1;
while ( regitr_overlap(tmp_itr) )
{
if ( tmp_itr->beg != rec->pos ) continue;
tgt_als_t *als = ®itr_payload(tmp_itr,tgt_als_t);
if ( als->used ) continue;
int nmatch_als = 0;
vcmp_t *vcmp = vcmp_init();
int ret = vcmp_set_ref(vcmp, rec->d.allele[0], als->allele[0]);
if ( ret==0 )
{
nmatch_als++;
if ( rec->n_allele > 1 && als->n > 1 )
{
for (j=1; j<als->n; j++)
{
if ( vcmp_find_allele(vcmp, rec->d.allele+1, rec->n_allele-1, als->allele[j])>=0 ) nmatch_als++;
}
}
}
int als_indel = is_indel(als->n, als->allele) ? 1 : -1;
nmatch_als *= rec_indel*als_indel;
if ( nmatch_als > rec_tgt.nmatch_als || !rec_tgt.als )
{
rec_tgt.nmatch_als = nmatch_als;
rec_tgt.als = als;
rec_tgt.ibuf = i;
}
vcmp_destroy(vcmp);
}
}
regitr_destroy(tmp_itr);
args->aux.tgt_als = rec_tgt.als;
if ( rec_tgt.als ) rec_tgt.als->used = 1;
rec = vcfbuf_remove(args->vcfbuf, rec_tgt.ibuf);
return rec;
}
static void init_data(args_t *args)
{
args->aux.srs = bcf_sr_init();
// Open files for input and output, initialize structures
if ( args->targets )
{
args->tgt_idx = regidx_init(args->targets, tgt_parse, args->aux.flag&CALL_CONSTR_ALLELES ? tgt_free : (regidx_free_f) NULL, sizeof(tgt_als_t), args->aux.flag&CALL_CONSTR_ALLELES ? args : NULL);
args->tgt_itr = regitr_init(args->tgt_idx);
args->tgt_itr_tmp = regitr_init(args->tgt_idx);
}
if ( args->regions )
{
bcf_sr_set_opt(args->aux.srs,BCF_SR_REGIONS_OVERLAP,args->regions_overlap);
if ( bcf_sr_set_regions(args->aux.srs, args->regions, args->regions_is_file)<0 )
error("Failed to read the regions: %s\n", args->regions);
}
if ( !bcf_sr_add_reader(args->aux.srs, args->bcf_fname) )
error("Failed to read from %s: %s\n", !strcmp("-",args->bcf_fname)?"standard input":args->bcf_fname,bcf_sr_strerror(args->aux.srs->errnum));
args->aux.hdr = bcf_sr_get_header(args->aux.srs,0);
int i;
if ( args->samples_fname )
{
set_samples(args, args->samples_fname, args->samples_is_file);
if ( args->aux.flag&CALL_CONSTR_TRIO )
{
if ( 3*args->aux.nfams!=args->nsamples ) error("Expected only trios in %s, sorry!\n", args->samples_fname);
fprintf(stderr,"Detected %d samples in %d trio families\n", args->nsamples,args->aux.nfams);
}
}
if ( args->ploidy )
{
args->nsex = ploidy_nsex(args->ploidy);
args->sex2ploidy = (int*) calloc(args->nsex,sizeof(int));
args->sex2ploidy_prev = (int*) calloc(args->nsex,sizeof(int));
if ( !args->nsamples )
{
args->nsamples = bcf_hdr_nsamples(args->aux.hdr);
args->sample2sex = (int*) malloc(sizeof(int)*args->nsamples);
for (i=0; i<args->nsamples; i++) args->sample2sex[i] = args->nsex - 1;
}
}
if ( args->nsamples )
{
args->aux.ploidy = (uint8_t*) malloc(args->nsamples);
for (i=0; i<args->nsamples; i++) args->aux.ploidy[i] = ploidy_max(args->ploidy);
for (i=0; i<args->nsex; i++) args->sex2ploidy_prev[i] = ploidy_max(args->ploidy);
for (i=0; i<args->nsamples; i++)
if ( args->sample2sex[i] >= args->nsex ) args->sample2sex[i] = args->nsex - 1;
}
if ( args->gvcf )
{
int id = bcf_hdr_id2int(args->aux.hdr,BCF_DT_ID,"DP");
if ( id<0 || !bcf_hdr_idinfo_exists(args->aux.hdr,BCF_HL_FMT,id) ) error("--gvcf output mode requires FORMAT/DP tag, which is not present in the input header\n");
gvcf_update_header(args->gvcf, args->aux.hdr);
}
if ( args->samples_map )
{
args->aux.hdr = bcf_hdr_subset(bcf_sr_get_header(args->aux.srs,0), args->nsamples, args->samples, args->samples_map);
if ( !args->aux.hdr ) error("Error occurred while subsetting samples\n");
for (i=0; i<args->nsamples; i++)
if ( args->samples_map[i]<0 ) error("No such sample: %s\n", args->samples[i]);
if ( !bcf_hdr_nsamples(args->aux.hdr) ) error("No matching sample found\n");
}
else
{
args->aux.hdr = bcf_hdr_dup(bcf_sr_get_header(args->aux.srs,0));
if ( args->samples )
{
for (i=0; i<args->nsamples; i++)
if ( bcf_hdr_id2int(args->aux.hdr,BCF_DT_SAMPLE,args->samples[i])<0 )
error("No such sample: %s\n", args->samples[i]);
}
}
if ( args->aux.flag & CALL_CONSTR_ALLELES )
{
args->vcfbuf = vcfbuf_init(args->aux.hdr, 0);
vcfbuf_set(args->vcfbuf,VCFBUF_DUMMY,1);
}
char wmode[8];
set_wmode(wmode,args->output_type,args->output_fname,args->clevel);
args->out_fh = hts_open(args->output_fname ? args->output_fname : "-", wmode);
if ( args->out_fh == NULL ) error("Error: cannot write to \"%s\": %s\n", args->output_fname, strerror(errno));
if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads);
if ( args->flag & CF_QCALL )
return;
if ( args->flag & CF_MCALL )
mcall_init(&args->aux);
if ( args->flag & CF_CCALL )
ccall_init(&args->aux);
bcf_hdr_remove(args->aux.hdr, BCF_HL_INFO, "QS");
bcf_hdr_remove(args->aux.hdr, BCF_HL_INFO, "I16");
if (args->record_cmd_line) bcf_hdr_append_version(args->aux.hdr, args->argc, args->argv, "bcftools_call");
if ( bcf_hdr_write(args->out_fh, args->aux.hdr)!=0 ) error("[%s] Error: cannot write the header to %s\n", __func__,args->output_fname);
if ( init_index2(args->out_fh,args->aux.hdr,args->output_fname,
&args->index_fn, args->write_index)<0 )
error("Error: failed to initialise index for %s\n",args->output_fname);
if ( args->flag&CF_INS_MISSED ) init_missed_line(args);
}
static void destroy_data(args_t *args)
{
if ( args->vcfbuf ) vcfbuf_destroy(args->vcfbuf);
if ( args->tgt_idx )
{
regidx_destroy(args->tgt_idx);
regitr_destroy(args->tgt_itr);
regitr_destroy(args->tgt_itr_tmp);
if ( args->tgt_itr_prev ) regitr_destroy(args->tgt_itr_prev);
}
if ( args->flag & CF_CCALL ) ccall_destroy(&args->aux);
else if ( args->flag & CF_MCALL ) mcall_destroy(&args->aux);
else if ( args->flag & CF_QCALL ) qcall_destroy(&args->aux);
int i;
if ( args->samples )
{
for (i=0; i<args->nsamples; i++) free(args->samples[i]);
}
if ( args->aux.fams )
{
for (i=0; i<args->aux.nfams; i++) free(args->aux.fams[i].name);
free(args->aux.fams);
}
if ( args->missed_line ) bcf_destroy(args->missed_line);
ploidy_destroy(args->ploidy);
free(args->sex2ploidy);
free(args->sex2ploidy_prev);
free(args->samples);
free(args->samples_map);
free(args->sample2sex);
free(args->aux.ploidy);
free(args->str.s);
if ( args->gvcf ) gvcf_destroy(args->gvcf);
bcf_hdr_destroy(args->aux.hdr);
if ( args->write_index )
{
if ( bcf_idx_save(args->out_fh)<0 )
{
if ( hts_close(args->out_fh)!=0 ) error("Error: close failed .. %s\n", args->output_fname?args->output_fname:"stdout");
error("Error: cannot write to index %s\n", args->index_fn);
}
free(args->index_fn);
}
if ( hts_close(args->out_fh)!=0 ) error("[%s] Error: close failed .. %s\n", __func__,args->output_fname);
bcf_sr_destroy(args->aux.srs);
}
void parse_novel_rate(args_t *args, const char *str)
{
if ( sscanf(str,"%le,%le,%le",&args->aux.trio_Pm_SNPs,&args->aux.trio_Pm_del,&args->aux.trio_Pm_ins)==3 ) // explicit for all
{
args->aux.trio_Pm_SNPs = 1 - args->aux.trio_Pm_SNPs;
args->aux.trio_Pm_del = 1 - args->aux.trio_Pm_del;
args->aux.trio_Pm_ins = 1 - args->aux.trio_Pm_ins;
}
else if ( sscanf(str,"%le,%le",&args->aux.trio_Pm_SNPs,&args->aux.trio_Pm_del)==2 ) // dynamic for indels
{
args->aux.trio_Pm_SNPs = 1 - args->aux.trio_Pm_SNPs;
args->aux.trio_Pm_ins = -1; // negative value for dynamic calculation
}
else if ( sscanf(str,"%le",&args->aux.trio_Pm_SNPs)==1 ) // same for all
{
args->aux.trio_Pm_SNPs = 1 - args->aux.trio_Pm_SNPs;
args->aux.trio_Pm_del = -1;
args->aux.trio_Pm_ins = -1;
}
else error("Could not parse --novel-rate %s\n", str);
}
static void list_annotations(FILE *fp)
{
fprintf(fp,
"\n"
"Optional INFO annotations available with -m (\"INFO/\" prefix is optional):\n"
" INFO/PV4 .. P-values for strand bias, baseQ bias, mapQ bias and tail distance bias (Number=4,Type=Float)\n"
"\n"
"Optional FORMAT annotations available with -m (\"FORMAT/\" prefix is optional):\n"
" FORMAT/GQ .. Phred-scaled genotype quality (Number=1,Type=Integer)\n"
" FORMAT/GP .. Phred-scaled genotype posterior probabilities (Number=G,Type=Float)\n"
"\n");
}
static int parse_output_tags(const char *str)
{
int flag = 0;
const char *ss = str;
while ( *ss )
{
const char *se = ss;
while ( *se && *se!=',' ) se++;
if ( !strncasecmp(ss,"GQ",se-ss) || !strncasecmp(ss,"FORMAT/GQ",se-ss) || !strncasecmp(ss,"FMT/GQ",se-ss) ) flag |= CALL_FMT_GQ;
else if ( !strncasecmp(ss,"GP",se-ss) || !strncasecmp(ss,"FORMAT/GP",se-ss) || !strncasecmp(ss,"FMT/GP",se-ss) ) flag |= CALL_FMT_GP;
else if ( !strncasecmp(ss,"PV4",se-ss) || !strncasecmp(ss,"INFO/PV4",se-ss) ) flag |= CALL_FMT_PV4;
else
{
fprintf(stderr,"Could not parse \"%s\"\n", str);
exit(1);
}
if ( !*se ) break;
ss = se + 1;
}
return flag;
}
static void set_ploidy(args_t *args, bcf1_t *rec)
{
ploidy_query(args->ploidy,(char*)bcf_seqname(args->aux.hdr,rec),rec->pos,args->sex2ploidy,NULL,NULL);
int i;
for (i=0; i<args->nsex; i++)
if ( args->sex2ploidy[i]!=args->sex2ploidy_prev[i] ) break;
if ( i==args->nsex ) return; // ploidy same as previously
for (i=0; i<args->nsamples; i++)
{
if ( args->sample2sex[i]<0 )
args->aux.ploidy[i] = -1*args->sample2sex[i];
else
args->aux.ploidy[i] = args->sex2ploidy[args->sample2sex[i]];
}
int *tmp = args->sex2ploidy; args->sex2ploidy = args->sex2ploidy_prev; args->sex2ploidy_prev = tmp;
}
ploidy_t *init_ploidy(char *alias)
{
const ploidy_predef_t *pld = ploidy_predefs;
int detailed = 0, len = strlen(alias);
if ( alias[len-1]=='?' ) { detailed = 1; alias[len-1] = 0; }
while ( pld->alias && strcasecmp(alias,pld->alias) ) pld++;
if ( !pld->alias )
{
fprintf(stderr,"\nPRE-DEFINED PLOIDY FILES\n\n");
fprintf(stderr," * Columns are: CHROM,FROM,TO,SEX,PLOIDY\n");
fprintf(stderr," * Coordinates are 1-based inclusive.\n");
fprintf(stderr," * A '*' means any value not otherwise defined.\n\n");
pld = ploidy_predefs;
while ( pld->alias )
{
fprintf(stderr,"%s\n .. %s\n\n", pld->alias,pld->about);
if ( detailed )
fprintf(stderr,"%s\n", pld->ploidy);
pld++;
}
fprintf(stderr,"Run as --ploidy <alias> (e.g. --ploidy GRCh37).\n");
fprintf(stderr,"To see the detailed ploidy definition, append a question mark (e.g. --ploidy GRCh37?).\n");
fprintf(stderr,"\n");
exit(-1);
}
else if ( detailed )
{
fprintf(stderr,"%s", pld->ploidy);
exit(-1);
}
return ploidy_init_string(pld->ploidy,2);
}
static void usage(args_t *args)
{
fprintf(stderr, "\n");
fprintf(stderr, "About: SNP/indel variant calling from VCF/BCF. To be used in conjunction with bcftools mpileup.\n");
fprintf(stderr, " This command replaces the former \"bcftools view\" caller. Some of the original\n");
fprintf(stderr, " functionality has been temporarily lost in the process of transition to htslib,\n");
fprintf(stderr, " but will be added back on popular demand. The original calling model can be\n");
fprintf(stderr, " invoked with the -c option.\n");
fprintf(stderr, "Usage: bcftools call [options] <in.vcf.gz>\n");
fprintf(stderr, "\n");
fprintf(stderr, "File format options:\n");
fprintf(stderr, " --no-version Do not append version and command line to the header\n");
fprintf(stderr, " -o, --output FILE Write output to a file [standard output]\n");
fprintf(stderr, " -O, --output-type b|u|z|v Output type: 'b' compressed BCF; 'u' uncompressed BCF; 'z' compressed VCF; 'v' uncompressed VCF [v]\n");
fprintf(stderr, " -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]\n");
fprintf(stderr, " --ploidy ASSEMBLY[?] Predefined ploidy, 'list' to print available settings, append '?' for details [2]\n");
fprintf(stderr, " --ploidy-file FILE Space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY\n");
fprintf(stderr, " -r, --regions REGION Restrict to comma-separated list of regions\n");
fprintf(stderr, " -R, --regions-file FILE Restrict to regions listed in a file\n");
fprintf(stderr, " --regions-overlap 0|1|2 Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
fprintf(stderr, " -s, --samples LIST List of samples to include [all samples]\n");
fprintf(stderr, " -S, --samples-file FILE PED file or a file with an optional column with sex (see man page for details) [all samples]\n");
fprintf(stderr, " -t, --targets REGION Similar to -r but streams rather than index-jumps\n");
fprintf(stderr, " -T, --targets-file FILE Similar to -R but streams rather than index-jumps\n");
fprintf(stderr, " --threads INT Use multithreading with INT worker threads [0]\n");
fprintf(stderr, "\n");
fprintf(stderr, "Input/output options:\n");
fprintf(stderr, " -A, --keep-alts Keep all possible alternate alleles at variant sites\n");
fprintf(stderr, " -*, --keep-unseen-allele Keep the unobserved allele <*> or <NON_REF>\n");
fprintf(stderr, " -a, --annotate LIST Optional tags to output (lowercase allowed); '?' to list available tags\n");
fprintf(stderr, " -F, --prior-freqs AN,AC Use prior allele frequencies, determined from these pre-filled tags\n");
fprintf(stderr, " -G, --group-samples FILE|- Group samples by population (file with \"sample\\tgroup\") or \"-\" for single-sample calling.\n");
fprintf(stderr, " This requires FORMAT/QS or other Number=R,Type=Integer tag such as FORMAT/AD\n");
fprintf(stderr, " --group-samples-tag TAG The tag to use with -G, by default FORMAT/QS and FORMAT/AD are checked automatically\n");
fprintf(stderr, " -g, --gvcf INT,[...] Group non-variant sites into gVCF blocks by minimum per-sample DP\n");
fprintf(stderr, " -i, --insert-missed Output also sites missed by mpileup but present in -T\n");
fprintf(stderr, " -M, --keep-masked-ref Keep sites with masked reference allele (REF=N)\n");
fprintf(stderr, " -V, --skip-variants TYPE Skip indels/snps\n");
fprintf(stderr, " -v, --variants-only Output variant sites only\n");
fprintf(stderr, " -W, --write-index[=FMT] Automatically index the output files [off]\n");
fprintf(stderr, "\n");
fprintf(stderr, "Consensus/variant calling options:\n");
fprintf(stderr, " -c, --consensus-caller The original calling method (conflicts with -m)\n");
fprintf(stderr, " -C, --constrain STR One of: alleles, trio (see manual)\n");
fprintf(stderr, " -m, --multiallelic-caller Alternative model for multiallelic and rare-variant calling (conflicts with -c)\n");
fprintf(stderr, " -n, --novel-rate FLOAT,[...] Likelihood of novel mutation for constrained trio calling, see man page for details [1e-8,1e-9,1e-9]\n");
fprintf(stderr, " -p, --pval-threshold FLOAT Variant if P(ref|D)<FLOAT with -c [0.5]\n");
fprintf(stderr, " -P, --prior FLOAT Mutation rate (use bigger for greater sensitivity), use with -m [1.1e-3]\n");
fprintf(stderr, "\n");
fprintf(stderr, "Example:\n");
fprintf(stderr, " # See also http://samtools.github.io/bcftools/howtos/variant-calling.html\n");
fprintf(stderr, " bcftools mpileup -Ou -f reference.fa alignments.bam | bcftools call -mv -Ob -o calls.bcf\n");
// todo (and more)
// fprintf(stderr, "\nContrast calling and association test options:\n");
// fprintf(stderr, " -1 INT number of group-1 samples [0]\n");
// fprintf(stderr, " -C FLOAT posterior contrast for LRT<FLOAT and P(ref|D)<0.5 [%g]\n", args->aux.min_lrt);
// fprintf(stderr, " -U INT number of permutations for association testing (effective with -1) [0]\n");
// fprintf(stderr, " -X FLOAT only perform permutations for P(chi^2)<FLOAT [%g]\n", args->aux.min_perm_p);
fprintf(stderr, "\n");
exit(-1);
}
int main_vcfcall(int argc, char *argv[])
{
char *ploidy_fname = NULL, *ploidy = NULL;
args_t args;
memset(&args, 0, sizeof(args_t));
args.argc = argc; args.argv = argv;
args.aux.prior_type = -1;
args.aux.indel_frac = -1;
args.aux.theta = 1.1e-3;
args.aux.pref = 0.5;
args.aux.min_perm_p = 0.01;
args.aux.min_lrt = 1;
args.flag = CF_ACGT_ONLY;
args.output_fname = "-";
args.output_type = FT_VCF;
args.n_threads = 0;
args.record_cmd_line = 1;
args.aux.trio_Pm_SNPs = 1 - 1e-8;
args.aux.trio_Pm_ins = args.aux.trio_Pm_del = 1 - 1e-9;
args.regions_overlap = 1;
args.clevel = -1;
int c;
static struct option loptions[] =
{
{"help",no_argument,NULL,'h'},
{"format-fields",required_argument,NULL,'f'},
{"annotate",required_argument,NULL,'a'},
{"prior-freqs",required_argument,NULL,'F'},
{"gvcf",required_argument,NULL,'g'},
{"group-samples",required_argument,NULL,'G'},
{"group-samples-tag",required_argument,NULL,3},
{"output",required_argument,NULL,'o'},
{"output-type",required_argument,NULL,'O'},
{"regions",required_argument,NULL,'r'},
{"regions-file",required_argument,NULL,'R'},
{"regions-overlap",required_argument,NULL,4},
{"samples",required_argument,NULL,'s'},
{"samples-file",required_argument,NULL,'S'},
{"targets",required_argument,NULL,'t'},
{"targets-file",required_argument,NULL,'T'},
{"threads",required_argument,NULL,9},
{"keep-alts",no_argument,NULL,'A'},
{"keep-unseen-allele",no_argument,NULL,'*'},
{"insert-missed",no_argument,NULL,'i'},
{"skip-Ns",no_argument,NULL,'N'}, // now the new default
{"keep-masked-refs",no_argument,NULL,'M'},