forked from samtools/bcftools
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathmcall.c
1717 lines (1546 loc) · 64.1 KB
/
mcall.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
/* mcall.c -- multiallelic and rare variant calling.
Copyright (C) 2012-2016 Genome Research Ltd.
Author: Petr Danecek <pd3@sanger.ac.uk>
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 <math.h>
#include <htslib/kfunc.h>
#include <htslib/khash_str2int.h>
#include "call.h"
// Using priors for GTs does not seem to be mathematically justified. Although
// it seems effective in removing false calls, it also flips a significant
// proportion of HET genotypes. Better is to filter by FORMAT/GQ using
// `bcftools filter`.
#define USE_PRIOR_FOR_GTS 0
// Go with uniform PLs for samples with no coverage. If unset, missing
// genotypes is reported instead.
#define FLAT_PDG_FOR_MISSING 0
void qcall_init(call_t *call) { return; }
void qcall_destroy(call_t *call) { return; }
int qcall(call_t *call, bcf1_t *rec)
{
// QCall format:
// chromosome, position, reference allele, depth, mapping quality, 0, ..
error("TODO: qcall output\n");
return 0;
}
void call_init_pl2p(call_t *call)
{
int i;
for (i=0; i<256; i++)
call->pl2p[i] = pow(10., -i/10.);
}
// Macros for accessing call->trio and call->ntrio
#define FTYPE_222 0 // family type: all diploid
#define FTYPE_121 1 // chrX, the child is a boy
#define FTYPE_122 2 // chrX, a girl
#define FTYPE_101 3 // chrY, boy
#define FTYPE_100 4 // chrY, girl
#define GT_SKIP 0xf // empty genotype (chrY in females)
#define IS_POW2(x) (!((x) & ((x) - 1))) // zero is permitted
#define IS_HOM(x) IS_POW2(x)
// Pkij = P(k|i,j) tells how likely it is to be a het if the parents
// are homs etc. The consistency of i,j,k has been already checked.
// Parameters are alleles and ploidy of father, mother, kid
// Returns 2/Pkij.
int calc_Pkij(int fals, int mals, int kals, int fpl, int mpl, int kpl)
{
int als = fals|mals|kals;
if ( IS_HOM(als) ) return 2; // all are the same: child must be a HOM, P=1
if ( fpl==1 )
{
if ( kpl==1 ) // chr X, the child is a boy, the copy is inherited from the mother
{
if ( IS_HOM(mals) ) return 2; // 0 11 -> P(1) = 1
return 4; // 0 01 -> P(0) = P(1) = 1/2
}
// chr X, the child is a girl
if ( IS_HOM(mals) ) return 2; // 0 11 -> P(01) = 1
return 4; // 0 01 -> P(00) = P(01) = 1/2
}
if ( IS_HOM(fals) && IS_HOM(mals) ) return 2; // 00 11 01, the child must be a HET, P=1
if ( !IS_HOM(fals) && !IS_HOM(mals) )
{
if ( IS_HOM(kals) ) return 8; // 01 01 00 or 01 01 11, P(k=HOM) = 1/4
return 4; // 01 01 01, P(k=HET) = 1/2
}
return 4; // 00 01, P(k=HET) = P(k=HOM) = 1/2
}
// Initialize ntrio and trio: ntrio lists the number of possible
// genotypes given combination of haploid/diploid genomes and the
// number of alleles. trio lists allowed genotype combinations:
// 4bit: 2/Pkij, 4: father, 4: mother, 4: child
// See also mcall_call_trio_genotypes()
//
static void mcall_init_trios(call_t *call)
{
if ( call->prior_AN )
{
int id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,call->prior_AN);
if ( id==-1 ) error("No such tag \"%s\"\n", call->prior_AN);
if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,id) ) error("No such FORMAT tag \"%s\"\n", call->prior_AN);
id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,call->prior_AC);
if ( id==-1 ) error("No such tag \"%s\"\n", call->prior_AC);
if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,id) ) error("No such FORMAT tag \"%s\"\n", call->prior_AC);
}
// 23, 138, 478 possible diploid trio genotypes with 2, 3, 4 alleles
call->ntrio[FTYPE_222][2] = 15; call->ntrio[FTYPE_222][3] = 78; call->ntrio[FTYPE_222][4] = 250;
call->ntrio[FTYPE_121][2] = 8; call->ntrio[FTYPE_121][3] = 27; call->ntrio[FTYPE_121][4] = 64;
call->ntrio[FTYPE_122][2] = 8; call->ntrio[FTYPE_122][3] = 27; call->ntrio[FTYPE_122][4] = 64;
call->ntrio[FTYPE_101][2] = 2; call->ntrio[FTYPE_101][3] = 3; call->ntrio[FTYPE_101][4] = 4;
call->ntrio[FTYPE_100][2] = 2; call->ntrio[FTYPE_100][3] = 3; call->ntrio[FTYPE_100][4] = 4;
int nals, itype;
for (itype=0; itype<=4; itype++)
{
for (nals=2; nals<=4; nals++)
call->trio[itype][nals] = (uint16_t*) malloc(sizeof(uint16_t)*call->ntrio[itype][nals]);
}
// max 10 possible diploid genotypes
int gts[10];
for (nals=2; nals<=4; nals++)
{
int i,j,k, n = 0, ngts = 0;
for (i=0; i<nals; i++)
for (j=0; j<=i; j++)
gts[ngts++] = 1<<i | 1<<j;
// 222: all diploid
// i,j,k: father, mother, child
for (i=0; i<ngts; i++)
for (j=0; j<ngts; j++)
for (k=0; k<ngts; k++)
{
if ( ((gts[i]|gts[j])>s[k]) != gts[k] ) continue; // k not present in neither i nor j
if ( !(gts[i] & gts[k]) || !(gts[j] & gts[k]) ) continue; // one copy from father, one from mother
int Pkij = calc_Pkij(gts[i],gts[j],gts[k], 2,2,2);
call->trio[FTYPE_222][nals][n++] = Pkij<<12 | i<<8 | j<<4 | k; // father, mother, child
}
assert( n==call->ntrio[FTYPE_222][nals] );
// 121: chrX, boy
n = 0;
for (i=0; i<ngts; i++)
for (j=0; j<ngts; j++)
for (k=0; k<ngts; k++)
{
if ( !IS_HOM(gts[i]) || !IS_HOM(gts[k]) ) continue; // father nor boy can be diploid
if ( ((gts[i]|gts[j])>s[k]) != gts[k] ) continue;
if ( !(gts[j] & gts[k]) ) continue; // boy must inherit the copy from mother
int Pkij = calc_Pkij(gts[i],gts[j],gts[k], 1,2,1);
call->trio[FTYPE_121][nals][n++] = Pkij<<12 | i<<8 | j<<4 | k;
}
assert( n==call->ntrio[FTYPE_121][nals] );
// 122: chrX, girl
n = 0;
for (i=0; i<ngts; i++)
for (j=0; j<ngts; j++)
for (k=0; k<ngts; k++)
{
if ( !IS_HOM(gts[i]) ) continue;
if ( ((gts[i]|gts[j])>s[k]) != gts[k] ) continue;
if ( !(gts[i] & gts[k]) ) continue; // girl must inherit one copy from the father and one from the mother
if ( !(gts[j] & gts[k]) ) continue;
int Pkij = calc_Pkij(gts[i],gts[j],gts[k], 1,2,2);
call->trio[FTYPE_122][nals][n++] = Pkij<<12 | i<<8 | j<<4 | k;
}
assert( n==call->ntrio[FTYPE_122][nals] );
// 101: chrY, boy
n = 0;
for (i=0; i<ngts; i++)
for (k=0; k<ngts; k++)
{
if ( !IS_HOM(gts[i]) || !IS_HOM(gts[k]) ) continue;
if ( (gts[i]>s[k]) != gts[k] ) continue;
call->trio[FTYPE_101][nals][n++] = 1<<12 | i<<8 | GT_SKIP<<4 | k;
}
assert( n==call->ntrio[FTYPE_101][nals] );
// 100: chrY, girl
n = 0;
for (i=0; i<ngts; i++)
{
if ( !IS_POW2(gts[i]) ) continue;
call->trio[FTYPE_100][nals][n++] = 1<<12 | i<<8 | GT_SKIP<<4 | GT_SKIP;
}
assert( n==call->ntrio[FTYPE_100][nals] );
}
call->GLs = (double*) calloc(bcf_hdr_nsamples(call->hdr)*10,sizeof(double));
int i, j;
for (i=0; i<call->nfams; i++)
{
family_t *fam = &call->fams[i];
int ploidy[3];
for (j=0; j<3; j++)
ploidy[j] = call->ploidy[fam->sample[j]];
if ( ploidy[FATHER]==2 ) // not X, not Y
{
if ( ploidy[MOTHER]!=2 || ploidy[CHILD]!=2 )
error("Incorrect ploidy: %d %d %d\n", ploidy[FATHER],ploidy[MOTHER],ploidy[CHILD]);
fam->type = FTYPE_222;
continue;
}
if ( ploidy[FATHER]!=1 || ploidy[MOTHER]==1 )
error("Incorrect ploidy: %d %d %d\n", ploidy[FATHER],ploidy[MOTHER],ploidy[CHILD]);
if ( ploidy[MOTHER]==2 ) // X
{
if ( ploidy[CHILD]==0 )
error("Incorrect ploidy: %d %d %d\n", ploidy[FATHER],ploidy[MOTHER],ploidy[CHILD]);
fam->type = ploidy[CHILD]==2 ? FTYPE_122 : FTYPE_121; // a girl or a boy
}
else // Y
{
if ( ploidy[CHILD]==2 )
error("Incorrect ploidy: %d %d %d\n", ploidy[FATHER],ploidy[MOTHER],ploidy[CHILD]);
fam->type = ploidy[CHILD]==0 ? FTYPE_100 : FTYPE_101; // a girl or a boy
}
}
}
static void mcall_destroy_trios(call_t *call)
{
int i, j;
for (i=2; i<=4; i++)
for (j=0; j<=4; j++)
free(call->trio[j][i]);
}
static void init_sample_groups(call_t *call)
{
int i, nsmpl = bcf_hdr_nsamples(call->hdr);
if ( !call->sample_groups )
{
// standard pooled calling, all samples in the same group
grp_t *grps = &call->smpl_grp;
grps->ngrp = 1;
grps->grp = (grp1_t*)calloc(grps->ngrp, sizeof(grp1_t));
grps->smpl2grp = (int*)calloc(nsmpl,sizeof(int));
}
else if ( !strcmp("-",call->sample_groups) )
{
// single-sample calling, each sample creates its own group
grp_t *grps = &call->smpl_grp;
grps->ngrp = nsmpl;
grps->grp = (grp1_t*)calloc(grps->ngrp, sizeof(grp1_t));
grps->smpl2grp = (int*)malloc(nsmpl*sizeof(int));
for (i=0; i<nsmpl; i++) grps->smpl2grp[i] = i;
}
else
{
int nlines;
char **lines = hts_readlist(call->sample_groups, 1, &nlines);
if ( !lines ) error("Could not read the file: %s\n", call->sample_groups);
uint32_t *smpl2grp1 = (uint32_t*)calloc(nsmpl,sizeof(uint32_t));
void *grp2idx = khash_str2int_init();
grp_t *grps = &call->smpl_grp;
for (i=0; i<nlines; i++)
{
char *ptr = lines[i];
while ( *ptr && *ptr!='\t' ) ptr++;
if ( !*ptr ) error("Could not parse the line in %s, expected a sample name followed by tab and a population name: %s\n",call->sample_groups,lines[i]);
*ptr = 0;
int ismpl = bcf_hdr_id2int(call->hdr, BCF_DT_SAMPLE, lines[i]);
if ( ismpl<0 ) continue;
if ( smpl2grp1[ismpl] ) error("Error: the sample \"%s\" is listed twice in %s\n", lines[i],call->sample_groups);
if ( !khash_str2int_has_key(grp2idx,ptr+1) )
{
khash_str2int_inc(grp2idx, ptr+1);
grps->ngrp++;
}
int igrp;
if ( khash_str2int_get(grp2idx, ptr+1, &igrp)!=0 ) error("This should not happen, fixme: %s\n",ptr+1);
smpl2grp1[ismpl] = igrp+1;
}
khash_str2int_destroy(grp2idx);
grps->grp = (grp1_t*)calloc(grps->ngrp, sizeof(grp1_t));
grps->smpl2grp = (int*)malloc(nsmpl*sizeof(int));
for (i=0; i<nsmpl; i++)
{
if ( !smpl2grp1[i] ) error("Error: The sample \"%s\" is not listed in %s\n",call->hdr->samples[i],call->sample_groups);
grps->smpl2grp[i] = smpl2grp1[i] - 1;
}
free(smpl2grp1);
for (i=0; i<nlines; i++) free(lines[i]);
free(lines);
}
}
static void destroy_sample_groups(call_t *call)
{
int i;
grp_t *grps = &call->smpl_grp;
for (i=0; i<grps->ngrp; i++)
free(grps->grp[i].qsum);
free(grps->grp);
free(grps->smpl2grp);
}
void mcall_init(call_t *call)
{
call_init_pl2p(call);
call->nals_map = 5;
call->als_map = (int*) malloc(sizeof(int)*call->nals_map);
call->npl_map = 5*(5+1)/2; // will be expanded later if necessary
call->pl_map = (int*) malloc(sizeof(int)*call->npl_map);
call->gts = (int32_t*) calloc(bcf_hdr_nsamples(call->hdr)*2,sizeof(int32_t)); // assuming at most diploid everywhere
if ( call->flag & CALL_CONSTR_TRIO )
{
call->cgts = (int32_t*) calloc(bcf_hdr_nsamples(call->hdr),sizeof(int32_t));
call->ugts = (int32_t*) calloc(bcf_hdr_nsamples(call->hdr),sizeof(int32_t));
mcall_init_trios(call);
bcf_hdr_append(call->hdr,"##FORMAT=<ID=CGT,Number=1,Type=Integer,Description=\"Constrained Genotype (0-based index to Number=G ordering).\">");
bcf_hdr_append(call->hdr,"##FORMAT=<ID=UGT,Number=1,Type=Integer,Description=\"Unconstrained Genotype (0-based index to Number=G ordering).\">");
}
if ( call->flag & CALL_CONSTR_ALLELES ) call->vcmp = vcmp_init();
bcf_hdr_append(call->hdr,"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
if ( call->output_tags & CALL_FMT_GQ )
bcf_hdr_append(call->hdr,"##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Phred-scaled Genotype Quality\">");
if ( call->output_tags & CALL_FMT_GP )
bcf_hdr_append(call->hdr,"##FORMAT=<ID=GP,Number=G,Type=Float,Description=\"Phred-scaled genotype posterior probabilities\">");
if ( call->output_tags & (CALL_FMT_GQ|CALL_FMT_GP) )
call->GQs = (int32_t*) malloc(sizeof(int32_t)*bcf_hdr_nsamples(call->hdr));
bcf_hdr_append(call->hdr,"##INFO=<ID=ICB,Number=1,Type=Float,Description=\"Inbreeding Coefficient Binomial test (bigger is better)\">");
bcf_hdr_append(call->hdr,"##INFO=<ID=HOB,Number=1,Type=Float,Description=\"Bias in the number of HOMs number (smaller is better)\">");
bcf_hdr_append(call->hdr,"##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Allele count in genotypes for each ALT allele, in the same order as listed\">");
bcf_hdr_append(call->hdr,"##INFO=<ID=AN,Number=1,Type=Integer,Description=\"Total number of alleles in called genotypes\">");
bcf_hdr_append(call->hdr,"##INFO=<ID=DP4,Number=4,Type=Integer,Description=\"Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases\">");
bcf_hdr_append(call->hdr,"##INFO=<ID=MQ,Number=1,Type=Integer,Description=\"Average mapping quality\">");
// init the prior
if ( call->theta>0 )
{
int i, n = 0;
if ( !call->ploidy ) n = 2*bcf_hdr_nsamples(call->hdr); // all are diploid
else
{
for (i=0; i<bcf_hdr_nsamples(call->hdr); i++)
n += call->ploidy[i];
}
// Watterson factor, here aM_1 = aM_2 = 1
double aM = 1;
for (i=2; i<n; i++) aM += 1./i;
call->theta *= aM;
if ( call->theta >= 1 )
{
fprintf(stderr,"The prior is too big (theta*aM=%.2f), going with 0.99\n", call->theta);
call->theta = 0.99;
}
call->theta = log(call->theta);
}
init_sample_groups(call);
}
void mcall_destroy(call_t *call)
{
destroy_sample_groups(call);
if (call->vcmp) vcmp_destroy(call->vcmp);
free(call->itmp);
mcall_destroy_trios(call);
free(call->GPs);
free(call->ADs);
free(call->GLs);
free(call->GQs);
free(call->anno16);
free(call->PLs);
free(call->als_map);
free(call->pl_map);
free(call->gts); free(call->cgts); free(call->ugts);
free(call->pdg);
free(call->als);
free(call->ac);
free(call->qsum);
return;
}
// Inits P(D|G): convert PLs from log space and normalize. In case of zero
// depth, missing PLs are all zero. In this case, pdg's are set to 0
// so that the corresponding genotypes can be set as missing and the
// qual calculation is not affected.
// Missing values are replaced by generic likelihoods when X (unseen allele) is
// present.
// NB: While the -m callig model uses the pdgs in canonical order,
// the original samtools -c calling code uses pdgs in reverse order (AA comes
// first, RR last).
// NB: Ploidy is not taken into account here, which is incorrect.
void set_pdg(double *pl2p, int *PLs, double *pdg, int n_smpl, int n_gt, int unseen)
{
int i, j, nals;
// find out the number of alleles, expecting diploid genotype likelihoods
bcf_gt2alleles(n_gt-1, &i, &nals);
assert( i==nals );
nals++;
for (i=0; i<n_smpl; i++)
{
double sum = 0;
for (j=0; j<n_gt; j++)
{
if ( PLs[j]==bcf_int32_vector_end )
{
// We expect diploid genotype likelihoods. If not diploid, treat as missing
j = 0;
break;
}
if ( PLs[j]==bcf_int32_missing ) break;
pdg[j] = PLs[j] < 256 ? pl2p[PLs[j]] : pow(10., -PLs[j]/10.);
sum += pdg[j];
}
if ( j==0 )
{
// First value is missing (LK of RR), this indicates that
// all values are missing.
j = sum = n_gt;
}
else if ( j<n_gt && unseen<0 )
{
// Some of the values are missing and the unseen allele LK is not
// available. In such a case, we set LK to a very small value.
sum = 0;
for (j=0; j<n_gt; j++)
{
assert( PLs[j]!=bcf_int32_vector_end );
if ( PLs[j]==bcf_int32_missing ) PLs[j] = 255;
pdg[j] = PLs[j] < 256 ? pl2p[PLs[j]] : pow(10., -PLs[j]/10.);
sum += pdg[j];
}
}
if ( j<n_gt )
{
// Missing values present, fill with unseen allele LK. This can be only
// as good as the merge was.
int ia,ib, k;
j = 0;
sum = 0;
for (ia=0; ia<nals; ia++)
{
for (ib=0; ib<=ia; ib++)
{
if ( PLs[j]==bcf_int32_missing )
{
k = bcf_alleles2gt(ia,unseen);
if ( PLs[k]==bcf_int32_missing ) k = bcf_alleles2gt(ib,unseen);
if ( PLs[k]==bcf_int32_missing ) k = bcf_alleles2gt(unseen,unseen);
if ( PLs[k]==bcf_int32_missing )
{
// The PLs for unseen allele X are not present as well as for ia, ib.
// This can happen with incremental calling, when one of the merged
// files had all alleles A,C,G,T, in such a case, X was not present.
// Use a very small value instead.
PLs[j] = 255;
}
else
PLs[j] = PLs[k];
}
pdg[j] = pl2p[ PLs[j] ];
sum += pdg[j];
j++;
}
}
}
// Normalize: sum_i pdg_i = 1
if ( sum==n_gt )
{
// all missing
#if FLAT_PDG_FOR_MISSING
for (j=0; j<n_gt; j++) pdg[j] = 1./n_gt;
#else
for (j=0; j<n_gt; j++) pdg[j] = 0;
#endif
}
else
for (j=0; j<n_gt; j++) pdg[j] /= sum;
PLs += n_gt;
pdg += n_gt;
}
}
// Create mapping between old and new (trimmed) alleles
void init_allele_trimming_maps(call_t *call, int als, int nals)
{
int i, j;
// als_map: old(i) -> new(j)
for (i=0, j=0; i<nals; i++)
{
if ( als & 1<<i ) call->als_map[i] = j++;
else call->als_map[i] = -1;
}
if ( !call->pl_map ) return;
// pl_map: new(k) -> old(l)
int k = 0, l = 0;
for (i=0; i<nals; i++)
{
for (j=0; j<=i; j++)
{
if ( (als & 1<<i) && (als & 1<<j) ) call->pl_map[k++] = l;
l++;
}
}
}
double binom_dist(int N, double p, int k)
{
int mean = (int) (N*p);
if ( mean==k ) return 1.0;
double log_p = (k-mean)*log(p) + (mean-k)*log(1.0-p);
if ( k > N - k ) k = N - k;
if ( mean > N - mean ) mean = N - mean;
if ( k < mean ) { int tmp = k; k = mean; mean = tmp; }
double diff = k - mean;
double val = 1.0;
int i;
for (i=0; i<diff; i++)
val = val * (N-mean-i) / (k-i);
return exp(log_p)/val;
}
// Inbreeding Coefficient, binomial test
float calc_ICB(int nref, int nalt, int nhets, int ndiploid)
{
if ( !nref || !nalt || !ndiploid ) return HUGE_VAL;
double fref = (double)nref/(nref+nalt); // fraction of reference allelels
double falt = (double)nalt/(nref+nalt); // non-ref als
double q = 2*fref*falt; // probability of a het, assuming HWE
double mean = q*ndiploid;
//fprintf(stderr,"\np=%e N=%d k=%d .. nref=%d nalt=%d nhets=%d ndiploid=%d\n", q,ndiploid,nhets, nref,nalt,nhets,ndiploid);
// Can we use normal approximation? The second condition is for performance only
// and is not well justified.
if ( (mean>10 && (1-q)*ndiploid>10 ) || ndiploid>200 )
{
//fprintf(stderr,"out: mean=%e p=%e\n", mean,exp(-0.5*(nhets-mean)*(nhets-mean)/(mean*(1-q))));
return exp(-0.5*(nhets-mean)*(nhets-mean)/(mean*(1-q)));
}
return binom_dist(ndiploid, q, nhets);
}
float calc_HOB(int nref, int nalt, int nhets, int ndiploid)
{
if ( !nref || !nalt || !ndiploid ) return HUGE_VAL;
double fref = (double)nref/(nref+nalt); // fraction of reference allelels
double falt = (double)nalt/(nref+nalt); // non-ref als
return fabs((double)nhets/ndiploid - 2*fref*falt);
}
/**
* log(sum_i exp(a_i))
*/
// static inline double logsumexp(double *vals, int nvals)
// {
// int i;
// double max_exp = vals[0];
// for (i=1; i<nvals; i++)
// if ( max_exp < vals[i] ) max_exp = vals[i];
// double sum = 0;
// for (i=0; i<nvals; i++)
// sum += exp(vals[i] - max_exp);
// return log(sum) + max_exp;
// }
/** log(exp(a)+exp(b)) */
static inline double logsumexp2(double a, double b)
{
if ( a>b )
return log(1 + exp(b-a)) + a;
else
return log(1 + exp(a-b)) + b;
}
// Macro to set the most likely alleles
#define UPDATE_MAX_LKs(als,sum) { \
if ( max_lk<lk_tot ) { max_lk = lk_tot; max_als = (als); } \
if ( sum ) lk_sum = logsumexp2(lk_tot,lk_sum); \
}
#define SWAP(type_t,x,y) {type_t tmp; tmp = x; x = y; y = tmp; }
// Determine the most likely combination of alleles. In this implementation,
// at most tri-allelic sites are considered. Returns the number of alleles.
static int mcall_find_best_alleles(call_t *call, int nals, int *out_als)
{
int j;
int ia,ib,ic; // iterators over up to three alleles
int max_als=0; // most likely combination of alleles
double ref_lk = 0, max_lk = -HUGE_VAL; // likelihood of the reference and of most likely combination of alleles
double lk_sum = -HUGE_VAL; // for normalizing the likelihoods
int nsmpl = bcf_hdr_nsamples(call->hdr);
int ngts = nals*(nals+1)/2;
// Single allele
for (ia=0; ia<nals; ia++)
{
double lk_tot = 0;
int lk_tot_set = 0;
int iaa = (ia+1)*(ia+2)/2-1; // index in PL which corresponds to the homozygous "ia/ia" genotype
int isample;
double *pdg = call->pdg + iaa;
for (isample=0; isample<nsmpl; isample++)
{
if ( *pdg ) { lk_tot += log(*pdg); lk_tot_set = 1; }
pdg += ngts;
}
if ( ia==0 ) ref_lk = lk_tot; // likelihood of 0/0 for all samples
else lk_tot += call->theta; // the prior
UPDATE_MAX_LKs(1<<ia, ia>0 && lk_tot_set);
}
grp_t *grps = &call->smpl_grp;
// Two alleles
if ( nals>1 )
{
for (ia=0; ia<nals; ia++)
{
if ( grps->ngrp==1 && grps->grp[0].qsum[ia]==0 ) continue;
int iaa = (ia+1)*(ia+2)/2-1;
for (ib=0; ib<ia; ib++)
{
if ( grps->ngrp==1 && grps->grp[0].qsum[ib]==0 ) continue;
double lk_tot = 0;
int lk_tot_set = 0;
int ia_cov = 0, ib_cov = 0;
for (j=0; j<grps->ngrp; j++)
{
grp1_t *grp = &grps->grp[j];
if ( grp->qsum[ia] ) ia_cov = 1;
if ( grp->qsum[ib] ) ib_cov = 1;
if ( !grp->qsum[ia] && !grp->qsum[ib] ) { grp->dp = 0; continue; }
grp->dp = 1;
grp->fa = grp->qsum[ia]/(grp->qsum[ia]+grp->qsum[ib]);
grp->fb = grp->qsum[ib]/(grp->qsum[ia]+grp->qsum[ib]);
grp->fa2 = grp->fa*grp->fa;
grp->fb2 = grp->fb*grp->fb;
grp->fab = 2*grp->fa*grp->fb;
}
if ( !ia_cov || !ib_cov ) continue;
int isample, ibb = (ib+1)*(ib+2)/2-1, iab = iaa - ia + ib;
double *pdg = call->pdg;
for (isample=0; isample<nsmpl; isample++)
{
grp1_t *grp = &grps->grp[grps->smpl2grp[isample]];
if ( !grp->dp ) continue;
double val = 0;
if ( !call->ploidy || call->ploidy[isample]==2 )
val = grp->fa2*pdg[iaa] + grp->fb2*pdg[ibb] + grp->fab*pdg[iab];
else if ( call->ploidy && call->ploidy[isample]==1 )
val = grp->fa*pdg[iaa] + grp->fb*pdg[ibb];
if ( val ) { lk_tot += log(val); lk_tot_set = 1; }
pdg += ngts;
}
if ( ia!=0 ) lk_tot += call->theta; // the prior
if ( ib!=0 ) lk_tot += call->theta;
UPDATE_MAX_LKs(1<<ia|1<<ib, lk_tot_set);
}
}
}
// Three alleles
if ( nals>2 )
{
for (ia=0; ia<nals; ia++)
{
if ( grps->ngrp==1 && grps->grp[0].qsum[ia]==0 ) continue;
int iaa = (ia+1)*(ia+2)/2-1;
for (ib=0; ib<ia; ib++)
{
if ( grps->ngrp==1 && grps->grp[0].qsum[ib]==0 ) continue;
int ibb = (ib+1)*(ib+2)/2-1;
int iab = iaa - ia + ib;
for (ic=0; ic<ib; ic++)
{
if ( grps->ngrp==1 && grps->grp[0].qsum[ic]==0 ) continue;
double lk_tot = 0;
int lk_tot_set = 1;
int ia_cov = 0, ib_cov = 0, ic_cov = 0;
for (j=0; j<grps->ngrp; j++)
{
grp1_t *grp = &grps->grp[j];
if ( grp->qsum[ia] ) ia_cov = 1;
if ( grp->qsum[ib] ) ib_cov = 1;
if ( grp->qsum[ic] ) ic_cov = 1;
if ( !grp->qsum[ia] && !grp->qsum[ib] && !grp->qsum[ic] ) { grp->dp = 0; continue; }
grp->dp = 1;
grp->fa = grp->qsum[ia]/(grp->qsum[ia]+grp->qsum[ib]+grp->qsum[ic]);
grp->fb = grp->qsum[ib]/(grp->qsum[ia]+grp->qsum[ib]+grp->qsum[ic]);
grp->fc = grp->qsum[ic]/(grp->qsum[ia]+grp->qsum[ib]+grp->qsum[ic]);
grp->fa2 = grp->fa*grp->fa;
grp->fb2 = grp->fb*grp->fb;
grp->fc2 = grp->fc*grp->fc;
grp->fab = 2*grp->fa*grp->fb, grp->fac = 2*grp->fa*grp->fc, grp->fbc = 2*grp->fb*grp->fc;
}
if ( !ia_cov || !ib_cov || !ic_cov ) continue;
int isample, icc = (ic+1)*(ic+2)/2-1;
int iac = iaa - ia + ic, ibc = ibb - ib + ic;
double *pdg = call->pdg;
for (isample=0; isample<nsmpl; isample++)
{
grp1_t *grp = &grps->grp[grps->smpl2grp[isample]];
if ( !grp->dp ) continue;
double val = 0;
if ( !call->ploidy || call->ploidy[isample]==2 )
val = grp->fa2*pdg[iaa] + grp->fb2*pdg[ibb] + grp->fc2*pdg[icc] + grp->fab*pdg[iab] + grp->fac*pdg[iac] + grp->fbc*pdg[ibc];
else if ( call->ploidy && call->ploidy[isample]==1 )
val = grp->fa*pdg[iaa] + grp->fb*pdg[ibb] + grp->fc*pdg[icc];
if ( val ) { lk_tot += log(val); lk_tot_set = 1; }
pdg += ngts;
}
if ( ia!=0 ) lk_tot += call->theta; // the prior
if ( ib!=0 ) lk_tot += call->theta; // the prior
if ( ic!=0 ) lk_tot += call->theta; // the prior
UPDATE_MAX_LKs(1<<ia|1<<ib|1<<ic, lk_tot_set);
}
}
}
}
call->ref_lk = ref_lk;
call->lk_sum = lk_sum;
*out_als = max_als;
int i, n = 0;
for (i=0; i<nals; i++) if ( max_als & 1<<i) n++;
return n;
}
static void mcall_set_ref_genotypes(call_t *call, int nals)
{
int i;
int ngts = nals*(nals+1)/2;
int nsmpl = bcf_hdr_nsamples(call->hdr);
for (i=0; i<nals; i++) call->ac[i] = 0;
call->nhets = 0;
call->ndiploid = 0;
// Set all genotypes to 0/0 or 0
int *gts = call->gts;
double *pdg = call->pdg;
int isample;
for (isample = 0; isample < nsmpl; isample++)
{
int ploidy = call->ploidy ? call->ploidy[isample] : 2;
for (i=0; i<ngts; i++) if ( pdg[i]!=0.0 ) break;
if ( i==ngts || !ploidy )
{
gts[0] = bcf_gt_missing;
gts[1] = ploidy==2 ? bcf_gt_missing : bcf_int32_vector_end;
}
else
{
gts[0] = bcf_gt_unphased(0);
gts[1] = ploidy==2 ? bcf_gt_unphased(0) : bcf_int32_vector_end;
call->ac[0] += ploidy;
}
gts += 2;
pdg += ngts;
}
}
static void mcall_call_genotypes(call_t *call, bcf1_t *rec, int nals, int nout_als, int out_als)
{
int ia, ib, i;
int ngts = nals*(nals+1)/2;
int nsmpl = bcf_hdr_nsamples(call->hdr);
int nout_gts = nout_als*(nout_als+1)/2;
hts_expand(float,nout_gts*nsmpl,call->nGPs,call->GPs);
for (i=0; i<nout_als; i++) call->ac[i] = 0;
call->nhets = 0;
call->ndiploid = 0;
#if USE_PRIOR_FOR_GTS
float prior = exp(call->theta);
#endif
float *gps = call->GPs - nout_gts;
double *pdg = call->pdg - ngts;
int *gts = call->gts - 2;
int isample;
for (isample = 0; isample < nsmpl; isample++)
{
int ploidy = call->ploidy ? call->ploidy[isample] : 2;
assert( ploidy>=0 && ploidy<=2 );
pdg += ngts;
gts += 2;
gps += nout_gts;
if ( !ploidy )
{
gts[0] = bcf_gt_missing;
gts[1] = bcf_int32_vector_end;
gps[0] = -1;
continue;
}
#if !FLAT_PDG_FOR_MISSING
// Skip samples with zero depth, they have all pdg's equal to 0
for (i=0; i<ngts; i++) if ( pdg[i]!=0.0 ) break;
if ( i==ngts )
{
gts[0] = bcf_gt_missing;
gts[1] = ploidy==2 ? bcf_gt_missing : bcf_int32_vector_end;
gps[0] = -1;
continue;
}
#endif
if ( ploidy==2 ) call->ndiploid++;
// Default fallback for the case all LKs are the same
gts[0] = bcf_gt_unphased(0);
gts[1] = ploidy==2 ? bcf_gt_unphased(0) : bcf_int32_vector_end;
// Non-zero depth, determine the most likely genotype
grp1_t *grp = &call->smpl_grp.grp[call->smpl_grp.smpl2grp[isample]];
double best_lk = 0;
for (ia=0; ia<nals; ia++)
{
if ( !(out_als & 1<<ia) ) continue; // ia-th allele not in the final selection, skip
int iaa = (ia+1)*(ia+2)/2-1; // PL index of the ia/ia genotype
double lk = ploidy==2 ? pdg[iaa]*grp->qsum[ia]*grp->qsum[ia] : pdg[iaa]*grp->qsum[ia];
#if USE_PRIOR_FOR_GTS
if ( ia!=0 ) lk *= prior;
#endif
int igt = ploidy==2 ? bcf_alleles2gt(call->als_map[ia],call->als_map[ia]) : call->als_map[ia];
gps[igt] = lk;
if ( best_lk < lk )
{
best_lk = lk;
gts[0] = bcf_gt_unphased(call->als_map[ia]);
}
}
if ( ploidy==2 )
{
gts[1] = gts[0];
for (ia=0; ia<nals; ia++)
{
if ( !(out_als & 1<<ia) ) continue;
int iaa = (ia+1)*(ia+2)/2-1;
for (ib=0; ib<ia; ib++)
{
if ( !(out_als & 1<<ib) ) continue;
int iab = iaa - ia + ib;
double lk = 2*pdg[iab]*grp->qsum[ia]*grp->qsum[ib];
#if USE_PRIOR_FOR_GTS
if ( ia!=0 ) lk *= prior;
if ( ib!=0 ) lk *= prior;
#endif
int igt = bcf_alleles2gt(call->als_map[ia],call->als_map[ib]);
gps[igt] = lk;
if ( best_lk < lk )
{
best_lk = lk;
gts[0] = bcf_gt_unphased(call->als_map[ib]);
gts[1] = bcf_gt_unphased(call->als_map[ia]);
}
}
}
if ( gts[0] != gts[1] ) call->nhets++;
}
else
gts[1] = bcf_int32_vector_end;
call->ac[ bcf_gt_allele(gts[0]) ]++;
if ( gts[1]!=bcf_int32_vector_end ) call->ac[ bcf_gt_allele(gts[1]) ]++;
}
if ( call->output_tags & (CALL_FMT_GQ|CALL_FMT_GP) )
{
double max, sum;
for (isample=0; isample<nsmpl; isample++)
{
gps = call->GPs + isample*nout_gts;
int nmax;
if ( call->ploidy )
{
if ( call->ploidy[isample]==2 ) nmax = nout_gts;
else if ( call->ploidy[isample]==1 ) nmax = nout_als;
else nmax = 0;
}
else nmax = nout_gts;
max = gps[0];
if ( max<0 || nmax==0 )
{
// no call
if ( call->output_tags & CALL_FMT_GP )
{
for (i=0; i<nmax; i++) gps[i] = 0;
if ( nmax==0 ) { bcf_float_set_missing(gps[i]); nmax++; }
if ( nmax < nout_gts ) bcf_float_set_vector_end(gps[nmax]);
}
call->GQs[isample] = 0;
continue;
}
sum = gps[0];
for (i=1; i<nmax; i++)
{
if ( max < gps[i] ) max = gps[i];
sum += gps[i];
}
max = -4.34294*log(1 - max/sum);
call->GQs[isample] = max<=INT8_MAX ? max : INT8_MAX;
if ( call->output_tags & CALL_FMT_GP )
{
assert( max );
for (i=0; i<nmax; i++) gps[i] = (int)(-4.34294*log(gps[i]/sum));
if ( nmax < nout_gts ) bcf_float_set_vector_end(gps[nmax]);
}
}
}
if ( call->output_tags & CALL_FMT_GP )
bcf_update_format_float(call->hdr, rec, "GP", call->GPs, nsmpl*nout_gts);
if ( call->output_tags & CALL_FMT_GQ )
bcf_update_format_int32(call->hdr, rec, "GQ", call->GQs, nsmpl);
}
/**
Pm = P(mendelian) .. parameter to vary, 1-Pm is the probability of novel mutation.
When trio_Pm_ins is negative, Pm is calculated dynamically
according to indel length. For simplicity, only the
first ALT is considered.
Pkij = P(k|i,j) .. probability that the genotype combination i,j,k is consistent
with mendelian inheritance (the likelihood that offspring
of two HETs is a HOM is smaller than it being a HET)
P_uc(F=i,M=j,K=k) = P(F=i) . P(M=j) . P(K=k) .. unconstrained P
P_c(F=i,M=j,K=k) = P_uc . Pkij .. constrained P
P(F=i,M=j,K=k) = P_uc . (1 - Pm) + P_c . Pm
= P_uc . [1 - Pm + Pkij . Pm]
We choose genotype combination i,j,k which maximizes P(F=i,M=j,K=k). This
probability gives the quality GQ(Trio).
Individual qualities are calculated as
GQ(F=i,M=j,K=k) = P(F=i,M=j,K=k) / \sum_{x,y} P(F=i,M=x,K=y)
*/
static void mcall_call_trio_genotypes(call_t *call, bcf1_t *rec, int nals, int nout_als, int out_als)
{
int ia, ib, i;
int nsmpl = bcf_hdr_nsamples(call->hdr);
int ngts = nals*(nals+1)/2;
int nout_gts = nout_als*(nout_als+1)/2;
double *gls = call->GLs - nout_gts;
double *pdg = call->pdg - ngts;
// Calculate individuals' genotype likelihoods P(X=i)
int isample;
for (isample = 0; isample < nsmpl; isample++)
{
int ploidy = call->ploidy ? call->ploidy[isample] : 2;
int32_t *gts = call->ugts + isample;
gls += nout_gts;
pdg += ngts;
// Skip samples with all pdg's equal to 1. These have zero depth.
for (i=0; i<ngts; i++) if ( pdg[i]!=0.0 ) break;
if ( i==ngts || !ploidy )
{