-
Notifications
You must be signed in to change notification settings - Fork 0
/
bglvset.c
1406 lines (1312 loc) · 45.3 KB
/
bglvset.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
#include "bglvset.h"
int catchopts(optstruct *opstru, int oargc, char **oargv)
{
int c;
opterr = 0;
while ((c = getopt (oargc, oargv, "pci:m:o:v:")) != -1)
switch (c) {
case 'c': // no printing out of files, please. I.e. _C_ancel printing to file.
opstru->cflag = 1;
break;
case 's': // stats version, no tped is output. Principally to see how hets are called.
opstru->sflag = 1;
break;
case 'p': // confirm you are feeding phased GTs, this will set | instead of / in VCF.
opstru->pflag = 1;
break;
case 'i': // input file
opstru->iname = optarg;
break;
case 'v': // input file
opstru->vname = optarg;
break;
case 'm': // input file
opstru->mname = optarg; /* the tfam of fam file */
break;
case 'o': // input file
opstru->oname = optarg; /* the tfam of fam file */
break;
case '?':
if ((optopt == 'i') | (optopt =='m') | (optopt == 'o') | (optopt == 'v')) {
fprintf (stderr, "Option -%c requires a string.\n", optopt);
exit(EXIT_FAILURE);
}
default:
abort();
}
return 0;
}
unsigned givehtsz(unsigned mnf)
{
unsigned htsz=2*mnf/3;
// try to grab a prime ... well just avoid 5-multiples, 3-multiples, and evens
if(!(htsz%5))
htsz++; // incrment by 1 if multiple of 5
if(!(htsz%3))
htsz++;
if(!(htsz%2))
htsz++;
return htsz;
}
unsigned hashit(char *str, unsigned tsz) /* Dan Bernstein's one */
{
unsigned long hash = 5381;
int c;
char *tstr=str;
while ((c = *tstr++))
hash = ((hash << 5) + hash) + c; /* hash * 33 + c */
return hash % tsz;
}
void prtchaharr(snodm **stab, unsigned tsz) // print out mp_t on baiss of second (SNP name) hashing
{
unsigned i;
snodm *tsnod2;
printf("SNPNAME\tPOS\tA1\tA2\n");
for(i=0;i<tsz;++i) {
tsnod2=stab[i];
while(tsnod2) {
printf("%s\t%s\t%c\t%c\n", tsnod2->aw->aw[0]->w, tsnod2->aw->aw[1]->w, tsnod2->aw->aw[2]->w[0], tsnod2->aw->aw[3]->w[0]);
tsnod2=tsnod2->n;
}
printf("\n");
}
return;
}
void freechainharr(snodm **stab, size_t tsz)
{
int i;
snodm *tsnod0, *tsnod2;
for(i=0; i<tsz; ++i) {
if( (stab[i] != NULL) ) {
while( (stab[i]->n != NULL) ) {
tsnod0=stab[i];
tsnod2=stab[i]->n;
while((tsnod2->n != NULL) ){
tsnod0=tsnod2;
tsnod2=tsnod2->n;
}
free(tsnod0->n);
tsnod0->n=NULL;
}
free(stab[i]);
}
}
free(stab);
return;
}
snodm **hashmrk(aaw_c *maawc, unsigned tsz)
{
unsigned i;
snodm **stab=malloc(tsz*sizeof(snodm *));
for(i=0;i<tsz;++i)
stab[i]=NULL;
snodm *tsnod0, *tsnod2;
unsigned tint;
/* OK, we're going to loop through the map file container: i here follows the global SNP name index */
for(i=0; i< maawc->numl; ++i) {
tint=hashit(maawc->aaw[i]->aw[0]->w, tsz); // hash the snpname
if( (stab[tint] == NULL) ) { // nothing in that slot right now.
stab[tint]=malloc(sizeof(snodm));
stab[tint]->aw=maawc->aaw[i];
stab[tint]->idx=i;
stab[tint]->n=NULL;
continue;
}
tsnod2=stab[tint];
while( (tsnod2 != NULL) ) {
tsnod0=tsnod2;
tsnod2=tsnod2->n;
}
tsnod0->n=malloc(sizeof(snodm));
tsnod0->n->aw = maawc->aaw[i];
tsnod0->n->idx=i;
tsnod0->n->n=NULL;
}
return stab;
}
snodm **hashmrk2(aaw_c *maawc, unsigned tsz)
{
unsigned i;
snodm **stab=malloc(tsz*sizeof(snodm *));
for(i=0;i<tsz;++i)
stab[i]=NULL;
snodm *tsnod0, *tsnod2;
unsigned tint;
/* OK, we're going to loop through the map file container: i here follows the global SNP name index */
for(i=0; i< maawc->numl; ++i) {
if(maawc->aaw[i]->gd == 2) // it's a dupe
continue;
tint=hashit(maawc->aaw[i]->aw[0]->w, tsz); // hash the snpname
if( (stab[tint] == NULL) ) { // nothing in that slot right now.
stab[tint]=malloc(sizeof(snodm));
stab[tint]->aw=maawc->aaw[i];
stab[tint]->idx=i;
stab[tint]->n=NULL;
continue;
}
tsnod2=stab[tint];
while( (tsnod2 != NULL) ) {
tsnod0=tsnod2;
tsnod2=tsnod2->n;
}
tsnod0->n=malloc(sizeof(snodm));
tsnod0->n->aw = maawc->aaw[i];
tsnod0->n->idx=i;
tsnod0->n->n=NULL;
}
return stab;
}
snodm **hashmrk_nd(aaw_c *maawc, unsigned tsz) /* throw out positional dups */
{
unsigned i;
snodm **stab=malloc(tsz*sizeof(snodm *));
for(i=0;i<tsz;++i)
stab[i]=NULL;
snodm *tsnod0, *tsnod2;
boole pos_seen; // this position already seen.
unsigned tint;
/* OK, we're going to loop through the map file container: i here follows the global SNP name index */
for(i=0; i< maawc->numl; ++i) {
pos_seen=0;
tint=hashit(maawc->aaw[i]->aw[1]->w, tsz); // hash the position
if( (stab[tint] == NULL) ) { // nothing in that slot right now.
stab[tint]=malloc(sizeof(snodm));
stab[tint]->aw=maawc->aaw[i];
stab[tint]->idx=i;
stab[tint]->n=NULL;
continue;
}
tsnod2=stab[tint];
while( (tsnod2 != NULL) ) {
if( !(strcmp(tsnod2->aw->aw[1]->w, maawc->aaw[i]->aw[1]->w))) {
tsnod2->aw->gd=1; // means this already hashed line was first but has a dup
maawc->aaw[i]->gd=2; // means this unhashed line was second (or later) to a first dup.
pos_seen=1;
break;
}
tsnod0=tsnod2;
tsnod2=tsnod2->n;
}
if(pos_seen)
continue;
tsnod0->n=malloc(sizeof(snodm));
tsnod0->n->aw = maawc->aaw[i];
tsnod0->n->idx=i;
tsnod0->n->n=NULL;
}
return stab;
}
w_c *crea_wc(unsigned initsz)
{
w_c *wc=malloc(sizeof(w_c));
wc->lp1=initsz;
wc->w=malloc(wc->lp1*sizeof(char));
return wc;
}
void reall_wc(w_c **wc, unsigned *cbuf)
{
w_c *twc=*wc;
unsigned tcbuf=*cbuf;
tcbuf += CBUF;
twc->lp1=tcbuf;
twc->w=realloc(twc->w, tcbuf*sizeof(char));
*wc=twc; /* realloc can often change the ptr */
*cbuf=tcbuf;
return;
}
void norm_wc(w_c **wc)
{
w_c *twc=*wc;
twc->w=realloc(twc->w, twc->lp1*sizeof(char));
*wc=twc; /* realloc can often change the ptr */
return;
}
void free_wc(w_c **wc)
{
w_c *twc=*wc;
free(twc->w);
free(twc);
return;
}
aw_c *crea_awc(unsigned initsz)
{
int i;
aw_c *awc=malloc(sizeof(aw_c));
awc->ab=initsz;
awc->al=awc->ab;
awc->gd=0;
awc->gdn=0;
awc->aw=malloc(awc->ab*sizeof(w_c*));
for(i=0;i<awc->ab;++i)
awc->aw[i]=crea_wc(CBUF);
return awc;
}
void reall_awc(aw_c **awc, unsigned buf)
{
int i;
aw_c *tawc=*awc;
tawc->ab += buf;
tawc->al=tawc->ab;
tawc->aw=realloc(tawc->aw, tawc->ab*sizeof(aw_c*));
for(i=tawc->ab-buf;i<tawc->ab;++i)
tawc->aw[i]=crea_wc(CBUF);
*awc=tawc;
return;
}
void norm_awc(aw_c **awc)
{
int i;
aw_c *tawc=*awc;
/* free the individual w_c's */
for(i=tawc->al;i<tawc->ab;++i)
free_wc(tawc->aw+i);
/* now release the pointers to those freed w_c's */
tawc->aw=realloc(tawc->aw, tawc->al*sizeof(aw_c*));
*awc=tawc;
return;
}
void free_awc(aw_c **awc)
{
int i;
aw_c *tawc=*awc;
for(i=0;i<tawc->al;++i)
free_wc(tawc->aw+i);
free(tawc->aw); /* unbelieveable: I left this out, couldn't find where I leaking the memory! */
free(tawc);
return;
}
aaw_c *crea_aawc(unsigned initsz)
{
int i;
unsigned lbuf=initsz;
aaw_c *aawc=malloc(sizeof(aaw_c));
aawc->numl=0;
aawc->aaw=malloc(lbuf*sizeof(aw_c*));
for(i=0;i<initsz;++i)
aawc->aaw[i]=crea_awc(WABUF);
return aawc;
}
void free_aawc(aaw_c **aw)
{
int i;
aaw_c *taw=*aw;
for(i=0;i<taw->numl;++i) /* tried to release 1 more, no go */
free_awc(taw->aaw+i);
free(taw->aaw);
free(taw);
}
gt_t from2l(char A1, char A2)
{
/* return a gt type for two letters */
gt_t tgt; // The temporary GT
switch(A1) {
case 'A':
switch(A2){
case 'A':
tgt=AA; break;
case 'C':
tgt=AC; break;
case 'G':
tgt=AG; break;
case 'T':
tgt=AT; break;
case 'I': case 'D':
tgt=D1; break;
case 'N': case '0':
tgt=Z1; break;
default:
tgt=ZZ;
}
break;
case 'C':
switch(A2){
case 'A':
tgt=CA; break;
case 'C':
tgt=CC; break;
case 'G':
tgt=CG; break;
case 'T':
tgt=CT; break;
case 'I': case 'D':
tgt=D1; break;
case 'N': case '0':
tgt=Z1; break;
default:
tgt=ZZ;
}
break;
case 'G':
switch(A2){
case 'A':
tgt=GA; break;
case 'C':
tgt=GC; break;
case 'G':
tgt=GG; break;
case 'T':
tgt=GT; break;
case 'I': case 'D':
tgt=D1; break;
case 'N': case '0':
tgt=Z1; break;
default:
tgt=ZZ;
}
break;
case 'T':
switch(A2){
case 'A':
tgt=TA; break;
case 'C':
tgt=TC; break;
case 'G':
tgt=TG; break;
case 'T':
tgt=TT; break;
case 'I': case 'D':
tgt=D1; break;
case 'N': case '0':
tgt=Z1; break;
default:
tgt=ZZ;
}
break;
case 'D': case 'I':
switch(A2){
case 'A': case 'C': case 'G': case 'T':
tgt=D1; break;
default:
tgt=D2;
}
break;
case 'N': case '0':
switch(A2){
case 'A': case 'C': case 'G': case 'T':
tgt=Z1; break;
case 'I': case 'D':
/* special case where NI or ND occur: an ID was involced, so to speak */
tgt=D2; break;
default:
tgt=ZZ;
}
break;
default:
tgt=ZZ;
}
return tgt;
}
void prtaawcdbg(aaw_c *aawc)
{
int i, j, k;
printf("Legend: Begin with Line number, numwords in brackets, words uscore number, length of words:\n\n");
for(i=0;i<aawc->numl;++i) {
printf("l.%u(%u): ", i, aawc->aaw[i]->al);
for(j=0;j<aawc->aaw[i]->al;++j) {
printf("w_%u: ", j);
// if(aawc->aaw[i]->aw[j]->t == NUMS) {
// printf("NUM! ");
// continue;
// } else if(aawc->aaw[i]->aw[j]->t == PNI) {
// printf("PNI! ");
// continue;
// } else if(aawc->aaw[i]->aw[j]->t == STCP) {
// printf("STCP! ");
// continue;
// }
for(k=0;k<aawc->aaw[i]->aw[j]->lp1-1; k++)
putchar(aawc->aaw[i]->aw[j]->w[k]);
printf("/%u ", aawc->aaw[i]->aw[j]->lp1-1);
}
printf("\n");
}
}
void prtaawcdbg2(aaw_c *aawc)
{
int j, k;
size_t i;
printf("Legend: Begin with Line number, numwords in brackets, words uscore number, length of words:\n\n");
for(i=0;i<aawc->numl;++i) {
if(aawc->aaw[i]->aw[0]->w[0] == '#')
continue;
printf("%zu) IID: %s GT:", i, aawc->aaw[i]->aw[1]->w);
for(j=6;j<aawc->aaw[i]->al;j+=2) {
putchar(' ');
for(k=0;k<aawc->aaw[i]->aw[j]->lp1-1; k++)
putchar(aawc->aaw[i]->aw[j]->w[k]);
putchar('/');
for(k=0;k<aawc->aaw[i]->aw[j+1]->lp1-1; k++)
putchar(aawc->aaw[i]->aw[j+1]->w[k]);
}
printf("\n");
}
}
void statsaawc(aaw_c *aawc)
{
char a1, a2;
int j;
size_t i;
size_t a[12]; // counts which are "of interest"
size_t suma1good, suma1all, suma2good, suma2all;
float ra1, ra2, allra1=.0, allra2=.0;
printf("Samplename\t#A1==A\t#A1==C\t#A1==G\t#A1==T\t#A1==0\tA1==?\t #A2==A\t#A2==C\t#A2==G\t#A2==T\t#A2==0\tA2==?\tA1CR\tA2CR\n");
int numsamps =0; // because numl is not always numsamps due to # comment lines.
for(i=0;i<aawc->numl;++i) {
if(aawc->aaw[i]->aw[0]->w[0] == '#')
continue;
numsamps++;
for(j=0;j<12;++j)
a[j]= 0;
// OK now so now we have a match on the IIDs
// check num genos at very least
printf("%s\t", aawc->aaw[i]->aw[1]->w);
for(j=6;j<aawc->aaw[i]->al;j+=2) {
a1 = aawc->aaw[i]->aw[j]->w[0];
a2 = aawc->aaw[i]->aw[j+1]->w[0];
switch(a1) {
case 'A':
a[0]++; break;
case 'C':
a[1]++; break;
case 'G':
a[2]++; break;
case 'T':
a[3]++; break;
case '0':
a[4]++; break;
default:
a[5]++;
}
switch(a2) {
case 'A':
a[6]++; break;
case 'C':
a[7]++; break;
case 'G':
a[8]++; break;
case 'T':
a[9]++; break;
case '0':
a[10]++; break;
default:
a[11]++;
}
}
for(j=0;j<12;++j)
printf("%zu\t", a[j]);
suma1good=a[0]+a[1]+a[2]+a[3];
suma1all=suma1good+a[4]+a[5];
suma2good=a[6]+a[7]+a[8]+a[9];
suma2all=suma2good+a[10]+a[11];
ra1=(float)suma1good/suma1all;
ra2=(float)suma2good/suma2all;
allra1 += ra1;
allra2 += ra2;
printf("%4.4f\t%4.4f\n", ra1, ra2);
}
printf("Overall: AvgA1CR=%4.4f AvgA2CR=%4.4f\n", allra1/numsamps, allra2/numsamps);
}
void statsaawc2(aaw_c *aawc, float *allra1, float *allra2, int *retnumsamps)
{
char a1, a2;
int j;
size_t i;
size_t a[10]; // counts which are "of interest":
size_t suma1all, suma2all;
float ra1, ra2;
int numsamps = *retnumsamps; // because numl is not always numsamps due to # comment lines.
for(i=0;i<aawc->numl;++i) {
if(aawc->aaw[i]->aw[0]->w[0] == '#')
continue;
numsamps++;
for(j=0;j<10;++j)
a[j]= 0;
// OK now so now we have a match on the IIDs
// check num genos at very least
printf("%s\t", aawc->aaw[i]->aw[1]->w);
for(j=6;j<aawc->aaw[i]->al;j+=2) {
a1 = aawc->aaw[i]->aw[j]->w[0];
a2 = aawc->aaw[i]->aw[j+1]->w[0];
switch(a1) {
case 'A': case 'C': case 'G': case 'T': case 'a': case 'c': case 'g': case 't':
a[0]++; break;
case '0':
a[2]++; break;
case 'N': case 'n':
a[4]++; break;
case 'I': case 'D': case 'i': case 'd':
a[6]++; break;
default:
a[8]++;
}
switch(a2) {
case 'A': case 'C': case 'G': case 'T': case 'a': case 'c': case 'g': case 't':
a[1]++; break;
case '0':
a[3]++; break;
case 'N': case 'n':
a[5]++; break;
case 'I': case 'D': case 'i': case 'd':
a[7]++; break;
default:
a[9]++;
}
}
for(j=0;j<10;++j)
printf("%zu\t", a[j]);
suma1all=a[0]+a[2]+a[4]+a[6]+a[8];
suma2all=a[1]+a[3]+a[5]+a[7]+a[9];
ra1=(float)(a[0]+a[6])/suma1all;
printf("%4.4f\t", ra1);
ra2=(float)(a[1]+a[7])/suma2all;
printf("%4.4f\n", ra2);
/* now how we include IDs because hese are properly called. Often we don't used them though */
*allra1 += ra1;
*allra2 += ra2;
*retnumsamps=numsamps;
}
}
void prtaawcdata(aaw_c *aawc) /* print line and word details, but not the words themselves */
{
int i, j;
for(i=0;i<aawc->numl;++i) {
printf("L%u(%uw):", i, aawc->aaw[i]->al);
for(j=0;j<aawc->aaw[i]->al;++j) {
printf("l%ut", aawc->aaw[i]->aw[j]->lp1-1);
}
}
printf("\n");
}
void prtaawcplain(aaw_c *aawc) /* print line and word details, but not the words themselves */
{
int i, j;
int ll; /* length of line */
boole asamell=0; /* all same line length */
for(i=0;i<aawc->numl;++i) {
printf("L%u(%uw):", i, aawc->aaw[i]->al);
if(!i)
ll = aawc->aaw[i]->al;
else
if( ll != aawc->aaw[i]->al) {
asamell++;
printf("line %i, %i words\n", i, aawc->aaw[i]->al);
}
for(j=0;j<aawc->aaw[i]->al;++j)
printf((j!=aawc->aaw[i]->al-1)?"%s ":"%s\n", aawc->aaw[i]->aw[j]->w);
}
if(!asamell)
printf("All lines had same number of words (%i).\n", ll);
else
printf("Not all lines had same number of wordsi line 0 %i.\n", ll);
}
void prtaawc0(aaw_c *aawc, aaw_c *maawc, snodm **stab, unsigned htsz, char *tc)
{
int i, j, pos, unseencou=0;
int u2=0;
unsigned tint;
snodm *tsnod2;
boole seen;
for(i=2;i<aawc->numl;++i) {
seen = 0;
tint=hashit(aawc->aaw[i]->aw[1]->w, htsz); // hash the snpname
if(stab[tint] == NULL) {
u2++;
continue;
} else {
tsnod2=stab[tint];
while( (tsnod2 != NULL) ) {
if(!(strcmp(tsnod2->aw->aw[0]->w, aawc->aaw[i]->aw[1]->w))) {
seen =1;
pos=atoi(tsnod2->aw->aw[1]->w);
printf("%s ", tc);
printf("%s ", aawc->aaw[i]->aw[1]->w);
printf("%c ", '0');
printf("%i ", pos);
for(j=2;j<aawc->aaw[i]->al;++j)
printf((j!=aawc->aaw[i]->al-1)?"%s ":"%s\n", aawc->aaw[i]->aw[j]->w);
break;
}
tsnod2=tsnod2->n;
}
}
if(!seen) {
unseencou++;
// printf("%s ", aawc->aaw[i]->aw[1]->w);
}
}
if( u2 | unseencou)
printf("WARNING: #u2=%i unseen=%i\n", u2, unseencou);
return;
}
void prtaawc00(aaw_c *aawc, aaw_c *maawc, snodm **stab, aaw_c *vaawc, unsigned htsz, char *tc)
{
/* prints the BGL but with VCF interpolations ... a debugging function */
int i, j, pos, unseencou=0;
int u2=0;
unsigned tint;
snodm *tsnod2;
boole seen;
boole switchvgt;
int vi, vj;
char va1, va2; // these are a1 and a2 in the VCF file
for(i=2;i<aawc->numl;++i) {
vi=i+5;
seen = 0;
tint=hashit(aawc->aaw[i]->aw[1]->w, htsz); // hash the snpname
if(stab[tint] == NULL) {
u2++;
continue;
} else {
tsnod2=stab[tint];
while( (tsnod2 != NULL) ) {
if(!(strcmp(tsnod2->aw->aw[0]->w, aawc->aaw[i]->aw[1]->w))) {
seen =1;
pos=atoi(tsnod2->aw->aw[1]->w);
printf("%s ", tc);
printf("%s ", aawc->aaw[i]->aw[1]->w);
printf("%c ", '0');
printf("%i ", pos);
va1 = vaawc->aaw[vi]->aw[3]->w[0];
va2 = vaawc->aaw[vi]->aw[4]->w[0];
printf("%s ", vaawc->aaw[vi]->aw[3]->w);
printf("%s ", vaawc->aaw[vi]->aw[4]->w);
for(j=2;j<aawc->aaw[i]->al;++j) {
printf((j!=aawc->aaw[i]->al-1)?"%s ":"%s\n", aawc->aaw[i]->aw[j]->w);
vj=j/2+8;
switchvgt=0; // default don't switch VFCs GT
if(j%2==1) {
if(aawc->aaw[i]->aw[j]->w[0] == va1)
switchvgt=1;
if(switchvgt)
printf((j!=aawc->aaw[i]->al-1)?"%s ":"%s ", "1/0");
else
printf((j!=aawc->aaw[i]->al-1)?"%s ":"%s ", vaawc->aaw[vi]->aw[vj]->w);
}
}
break;
}
tsnod2=tsnod2->n;
}
}
if(!seen) {
unseencou++;
// printf("%s ", aawc->aaw[i]->aw[1]->w);
}
}
if( u2 | unseencou)
printf("WARNING: #u2=%i unseen=%i\n", u2, unseencou);
return;
}
void prtaawctp(aaw_c *aawc, aaw_c *maawc, snodm **stab, unsigned htsz, char *tc, char *fn)
{
int i, j, pos, unseencou=0;
int u2=0;
unsigned tint;
snodm *tsnod2;
boole seen;
FILE *fo=fopen(fn, "w");
for(i=2;i<aawc->numl;++i) {
seen = 0;
tint=hashit(aawc->aaw[i]->aw[1]->w, htsz); // hash the snpname
if(stab[tint] == NULL) {
u2++;
continue;
} else {
tsnod2=stab[tint];
while( (tsnod2 != NULL) ) {
if(!(strcmp(tsnod2->aw->aw[0]->w, aawc->aaw[i]->aw[1]->w))) {
seen =1;
pos=atoi(tsnod2->aw->aw[1]->w);
fprintf(fo, "%s ", tc);
fprintf(fo, "%s ", aawc->aaw[i]->aw[1]->w);
fprintf(fo, "%c ", '0');
fprintf(fo, "%i ", pos);
for(j=2;j<aawc->aaw[i]->al;++j)
fprintf(fo, (j!=aawc->aaw[i]->al-1)?"%s ":"%s\n", aawc->aaw[i]->aw[j]->w);
break;
}
tsnod2=tsnod2->n;
}
}
if(!seen) {
unseencou++;
// printf("%s ", aawc->aaw[i]->aw[1]->w);
}
}
if( u2 | unseencou)
fprintf(stderr, "WARNING: #u2=%i unseen=%i\n", u2, unseencou);
fclose(fo);
return;
}
void prt_tfc(aaw_c *tfc)
{
int i;
int ll0=0; /* length of line */
boole asamell0=0; /* all same line length? */
for(i=0;i<tfc->numl;++i) {
#ifdef DBG
printf("L%u(%uw):", i, tfc->aaw[i]->al);
#endif
if(!i)
ll0 = tfc->aaw[i]->al;
else
if( ll0 != tfc->aaw[i]->al) {
asamell0++;
#ifdef DBG
printf("exception - line %i, %i words\n", i, tfc->aaw[i]->al);
#endif
}
#ifdef DBG
for(j=0;j<tfc->aaw[i]->al;++j)
printf((j!=tfc->aaw[i]->al-1)?"%s ":"%s\n", tfc->aaw[i]->aw[j]->w);
#endif
}
if(!asamell0)
printf("All lines in .tfam had same number of words (%i).\n", ll0);
else
printf("Not all lines in .tfam had same number of words as line 0 %i.\n", ll0);
return;
}
void prt_vaawc(aaw_c *vaawc)
{
int i, j;
char fc; // this is the first char, useful to keep n case of distingusihig comments/vcf metadata.
for(i=0;i<vaawc->numl;++i) {
fc = vaawc->aaw[i]->aw[0]->w[0];
if(fc != '#') {
for(j=0;j<vaawc->aaw[i]->al;++j)
printf((j!=vaawc->aaw[i]->al-1)?"%s\t":"%s\n", vaawc->aaw[i]->aw[j]->w);
}
}
return;
}
void prt_vcf(aaw_c *vaawc, char *fname)
{
/* print out a new vcf file ... _2 appended to its basename */
int i, j;
char fc, sc; /* first char, second char: needed because sometimes VCF comen sneed tabs, othertimes not. */
FILE *fvp=fopen(fname, "w");
for(i=0;i<vaawc->numl;++i) {
fc = vaawc->aaw[i]->aw[0]->w[0];
sc = vaawc->aaw[i]->aw[0]->w[1];
for(j=0;j<vaawc->aaw[i]->al;++j) {
if(sc != '#')
fprintf(fvp, (j!=vaawc->aaw[i]->al-1)?"%s\t":"%s\n", vaawc->aaw[i]->aw[j]->w);
else
fprintf(fvp, (j!=vaawc->aaw[i]->al-1)?"%s ":"%s\n", vaawc->aaw[i]->aw[j]->w);
}
}
fclose(fvp);
return;
}
void prtvaawcvcf(aaw_c *aawc, aaw_c *maawc, snodm **stab, aaw_c *vaawc, unsigned htsz, char *tc, char *fname)
{
/* function not robust to different prints the BGL but with VCF interpolations ... a debugging function */
int i, j;
int u2=0;
unsigned tint;
unsigned commlines=0; // number of comments lines
snodm *tsnod2;
int bi, bj, bj2;
char va1, va2; // these are a1 and a2 in the VCF file
char ba1, ba2; // these are a1 and a2 in the BGL file
char fc, sc;
FILE *fvp=fopen(fname, "w");
for(i=0;i<vaawc->numl;++i) {
fc = vaawc->aaw[i]->aw[0]->w[0];
sc = vaawc->aaw[i]->aw[0]->w[1];
if(fc == '#') { // a comment, so print VCF as is.
commlines++;
for(j=0;j<vaawc->aaw[i]->al;++j) {
if(sc != '#')
fprintf(fvp, (j!=vaawc->aaw[i]->al-1)?"%s\t":"%s\n", vaawc->aaw[i]->aw[j]->w);
else
fprintf(fvp, (j!=vaawc->aaw[i]->al-1)?"%s ":"%s\n", vaawc->aaw[i]->aw[j]->w);
}
} else {
bi=i+2-commlines;
// seen = 0;
tint=hashit(aawc->aaw[bi]->aw[1]->w, htsz); // hash the snpname in the BGL file
// printf("BGL hash on %s\n", aawc->aaw[bi]->aw[1]->w);
if(stab[tint] == NULL) {
u2++;
continue;
} else {
tsnod2=stab[tint];
while( (tsnod2 != NULL) ) {
if(!(strcmp(tsnod2->aw->aw[0]->w, aawc->aaw[bi]->aw[1]->w))) {
// seen =1;
va1 = vaawc->aaw[i]->aw[3]->w[0];
va2 = vaawc->aaw[i]->aw[4]->w[0];
// fprintf(fvp, "VGT:%c%c ", va1, va2);
for(j=0;j<9;++j) // print straight VCF for first 9
fprintf(fvp, "%s\t", vaawc->aaw[i]->aw[j]->w);
for(j=9;j<vaawc->aaw[i]->al;++j) {
bj=2*(j-8);
bj2=bj+1;
ba1 = aawc->aaw[bi]->aw[bj]->w[0];
ba2 = aawc->aaw[bi]->aw[bj2]->w[0];
// fprintf(fvp, "BGT:%c%c ", ba1, ba2);
// if((ba1 == va1) & (ba2 == va2)) // heterozygous in order of va1 and va2
// fprintf(fvp, (j!=vaawc->aaw[i]->al-1)?"%s\t":"%s\n", vaawc->aaw[i]->aw[j]->w);
// else if( (ba2 == va1) & (ba1 == va2) ) // heterzygous in opposite order to va1, va2
if( (ba2 == va1) & (ba1 == va2) ) // heterzygous in opposite order to va1, va2
fprintf(fvp, (j!=vaawc->aaw[i]->al-1)?"%s\t":"%s\n", "1/0");
else // must be homozygous or in order heterozygous
fprintf(fvp, (j!=vaawc->aaw[i]->al-1)?"%s\t":"%s\n", vaawc->aaw[i]->aw[j]->w);
}
break;
}
tsnod2=tsnod2->n;
} // given an occupied location, go through all located SNPnames.
} // finished seeing if there's a hash location for marker on that SNP name
} // finished distinguishing between VCF comments and data
} // finished groing through all the lines in VCF
fclose(fvp);
return;
}
void prtvaawcvcfp(aaw_c *aawc, aaw_c *maawc, snodm **stab, aaw_c *vaawc, unsigned htsz, char *tc, char *fname)
{
/* phased version */
int i, j;
int u2=0;
unsigned tint;
unsigned commlines=0; // number of comments lines
snodm *tsnod2;
int bi, bj, bj2;
char va1, va2; // these are a1 and a2 in the VCF file
char ba1, ba2; // these are a1 and a2 in the BGL file
char fc, sc;
FILE *fvp=fopen(fname, "w");
for(i=0;i<vaawc->numl;++i) {
fc = vaawc->aaw[i]->aw[0]->w[0];
sc = vaawc->aaw[i]->aw[0]->w[1];
if(fc == '#') { // a comment, so print VCF as is.
commlines++;
for(j=0;j<vaawc->aaw[i]->al;++j) {
if(sc != '#')
fprintf(fvp, (j!=vaawc->aaw[i]->al-1)?"%s\t":"%s\n", vaawc->aaw[i]->aw[j]->w);
else
fprintf(fvp, (j!=vaawc->aaw[i]->al-1)?"%s ":"%s\n", vaawc->aaw[i]->aw[j]->w);
}
} else {
bi=i+2-commlines;
// seen = 0;
tint=hashit(aawc->aaw[bi]->aw[1]->w, htsz); // hash the snpname in the BGL file
// printf("BGL hash on %s\n", aawc->aaw[bi]->aw[1]->w);
if(stab[tint] == NULL) {
u2++;
continue;
} else {
tsnod2=stab[tint];
while( (tsnod2 != NULL) ) {
if(!(strcmp(tsnod2->aw->aw[0]->w, aawc->aaw[bi]->aw[1]->w))) {
// seen =1;
va1 = vaawc->aaw[i]->aw[3]->w[0];
va2 = vaawc->aaw[i]->aw[4]->w[0];
// fprintf(fvp, "VGT:%c%c ", va1, va2);
for(j=0;j<9;++j) // print straight VCF for first 9
fprintf(fvp, "%s\t", vaawc->aaw[i]->aw[j]->w);
for(j=9;j<vaawc->aaw[i]->al;++j) {
bj=2*(j-8);
bj2=bj+1;
ba1 = aawc->aaw[bi]->aw[bj]->w[0];
ba2 = aawc->aaw[bi]->aw[bj2]->w[0];
// fprintf(fvp, "BGT:%c%c ", ba1, ba2);
// if((ba1 == va1) & (ba2 == va2)) // heterozygous in order of va1 and va2
// fprintf(fvp, (j!=vaawc->aaw[i]->al-1)?"%s\t":"%s\n", vaawc->aaw[i]->aw[j]->w);
// else if( (ba2 == va1) & (ba1 == va2) ) // heterzygous in opposite order to va1, va2
if( (ba2 == va1) & (ba1 == va2) ) // heterzygous in opposite order to va1, va2
fprintf(fvp, (j!=vaawc->aaw[i]->al-1)?"%s\t":"%s\n", "1|0");
else if( (ba1 == va1) & (ba2 == va1) ) // homoz on a1
fprintf(fvp, (j!=vaawc->aaw[i]->al-1)?"%s\t":"%s\n", "0|0");
else if( (ba1 == va2) & (ba2 == va2) ) // homoz on a1
fprintf(fvp, (j!=vaawc->aaw[i]->al-1)?"%s\t":"%s\n", "1|1");
else if( (ba1 == va1) & (ba2 == va2) ) // heteroz on a1
fprintf(fvp, (j!=vaawc->aaw[i]->al-1)?"%s\t":"%s\n", "0|1");
}
break;
}
tsnod2=tsnod2->n;
} // given an occupied location, go through all located SNPnames.
} // finished seeing if there's a hash location for marker on that SNP name
} // finished distinguishing between VCF comments and data
} // finished groing through all the lines in VCF
fclose(fvp);
return;