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 void phase_update(args_t *args, bcf_hdr_t *hdr, bcf1_t *rec)
{
int i, nGTs = bcf_get_genotypes(hdr, rec, &args->GTa, &args->mGTa);
for (i=0; i<bcf_hdr_nsamples(hdr); i++)
{
if ( !args->swap_phase[i] ) continue;
int *gt = &args->GTa[i*2];
if ( gt[0]==bcf_gt_missing || gt[1]==bcf_int32_vector_end ) continue;
SWAP(int, gt[0], gt[1]);
gt[1] |= 1;
}
bcf_update_genotypes(hdr,rec,args->GTa,nGTs);
}
bcf1_t *process(bcf1_t *rec)
{
float af;
if(rec->n_allele==2) {
bcf_get_format_float(in_hdr, rec, "GL", &gl, &ngl);
assert(ngl==(3*n));
// bcf_get_genotypes(in_hdr, rec, >, &ngt);
// assert(ngt==(2*n));
af = estimate_gt();
// fprintf(stderr,"%d AF=%f\n",rec->pos+1,af);
bcf_update_format_float(out_hdr,rec,"DS",dosage,n);
bcf_update_info_float(out_hdr,rec,"AF",&af,1);
bcf_update_genotypes(out_hdr, rec, gt, ngt);
}
return rec;
}
bcf1_t *process(bcf1_t *rec)
{
int ngts = bcf_get_genotypes(in_hdr, rec, >s, &mgts);
int i, changed = 0;
for (i=0; i<ngts; i++)
{
if ( gts[i]==bcf_gt_missing )
{
gts[i] = new_gt;
changed++;
}
}
nchanged += changed;
if ( changed ) bcf_update_genotypes(out_hdr, rec, gts, ngts);
return rec;
}
void bcf_remove_alleles(const bcf_hdr_t *header, bcf1_t *line, int rm_mask)
{
int *map = (int*) calloc(line->n_allele, sizeof(int));
// create map of indexes from old to new ALT numbering and modify ALT
kstring_t str = {0,0,0};
kputs(line->d.allele[0], &str);
int nrm = 0, i,j; // i: ori alleles, j: new alleles
for (i=1, j=1; i<line->n_allele; i++)
{
if ( rm_mask & 1<<i )
{
// remove this allele
line->d.allele[i] = NULL;
nrm++;
continue;
}
kputc(',', &str);
kputs(line->d.allele[i], &str);
map[i] = j;
j++;
}
if ( !nrm ) { free(map); free(str.s); return; }
int nR_ori = line->n_allele;
int nR_new = line->n_allele-nrm;
assert(nR_new > 0); // should not be able to remove reference allele
int nA_ori = nR_ori-1;
int nA_new = nR_new-1;
int nG_ori = nR_ori*(nR_ori + 1)/2;
int nG_new = nR_new*(nR_new + 1)/2;
bcf_update_alleles_str(header, line, str.s);
// remove from Number=G, Number=R and Number=A INFO fields.
uint8_t *dat = NULL;
int mdat = 0, ndat = 0, mdat_bytes = 0, nret;
for (i=0; i<line->n_info; i++)
{
bcf_info_t *info = &line->d.info[i];
int vlen = bcf_hdr_id2length(header,BCF_HL_INFO,info->key);
if ( vlen!=BCF_VL_A && vlen!=BCF_VL_G && vlen!=BCF_VL_R ) continue; // no need to change
int type = bcf_hdr_id2type(header,BCF_HL_INFO,info->key);
if ( type==BCF_HT_FLAG ) continue;
int size = 1;
if ( type==BCF_HT_REAL || type==BCF_HT_INT ) size = 4;
mdat = mdat_bytes / size;
nret = bcf_get_info_values(header, line, bcf_hdr_int2id(header,BCF_DT_ID,info->key), (void**)&dat, &mdat, type);
mdat_bytes = mdat * size;
if ( nret<0 )
{
fprintf(stderr,"[%s:%d %s] Could not access INFO/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__,
bcf_hdr_int2id(header,BCF_DT_ID,info->key), bcf_seqname(header,line), line->pos+1, nret);
exit(1);
}
if ( type==BCF_HT_STR )
{
str.l = 0;
char *ss = (char*) dat, *se = (char*) dat;
if ( vlen==BCF_VL_A || vlen==BCF_VL_R )
{
int nexp, inc = 0;
if ( vlen==BCF_VL_A )
{
nexp = nA_ori;
inc = 1;
}
else
nexp = nR_ori;
for (j=0; j<nexp; j++)
{
if ( !*se ) break;
while ( *se && *se!=',' ) se++;
if ( rm_mask & 1<<(j+inc) )
{
if ( *se ) se++;
ss = se;
continue;
}
if ( str.l ) kputc(',',&str);
kputsn(ss,se-ss,&str);
if ( *se ) se++;
ss = se;
}
assert( j==nexp );
}
else // Number=G, assuming diploid genotype
{
int k = 0, n = 0;
for (j=0; j<nR_ori; j++)
{
for (k=0; k<=j; k++)
{
if ( !*se ) break;
while ( *se && *se!=',' ) se++;
n++;
if ( rm_mask & 1<<j || rm_mask & 1<<k )
{
if ( *se ) se++;
ss = se;
continue;
}
if ( str.l ) kputc(',',&str);
kputsn(ss,se-ss,&str);
if ( *se ) se++;
ss = se;
}
if ( !*se ) break;
}
assert( n=nG_ori );
}
nret = bcf_update_info(header, line, bcf_hdr_int2id(header,BCF_DT_ID,info->key), (void*)str.s, str.l, type);
if ( nret<0 )
{
fprintf(stderr,"[%s:%d %s] Could not update INFO/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__,
bcf_hdr_int2id(header,BCF_DT_ID,info->key), bcf_seqname(header,line), line->pos+1, nret);
exit(1);
}
continue;
}
if ( vlen==BCF_VL_A || vlen==BCF_VL_R )
{
int inc = 0, ntop;
if ( vlen==BCF_VL_A )
{
assert( nret==nA_ori );
ntop = nA_ori;
ndat = nA_new;
inc = 1;
}
else
{
assert( nret==nR_ori );
ntop = nR_ori;
ndat = nR_new;
}
int k = 0;
#define BRANCH(type_t,is_vector_end) \
{ \
type_t *ptr = (type_t*) dat; \
int size = sizeof(type_t); \
for (j=0; j<ntop; j++) /* j:ori, k:new */ \
{ \
if ( is_vector_end ) { memcpy(dat+k*size, dat+j*size, size); break; } \
if ( rm_mask & 1<<(j+inc) ) continue; \
if ( j!=k ) memcpy(dat+k*size, dat+j*size, size); \
k++; \
} \
}
switch (type)
{
case BCF_HT_INT: BRANCH(int32_t,ptr[j]==bcf_int32_vector_end); break;
case BCF_HT_REAL: BRANCH(float,bcf_float_is_vector_end(ptr[j])); break;
}
#undef BRANCH
}
else // Number=G
{
assert( nret==nG_ori );
int k, l_ori = -1, l_new = 0;
ndat = nG_new;
#define BRANCH(type_t,is_vector_end) \
{ \
type_t *ptr = (type_t*) dat; \
int size = sizeof(type_t); \
for (j=0; j<nR_ori; j++) \
{ \
for (k=0; k<=j; k++) \
{ \
l_ori++; \
if ( is_vector_end ) { memcpy(dat+l_new*size, dat+l_ori*size, size); break; } \
if ( rm_mask & 1<<j || rm_mask & 1<<k ) continue; \
if ( l_ori!=l_new ) memcpy(dat+l_new*size, dat+l_ori*size, size); \
l_new++; \
} \
} \
}
switch (type)
{
case BCF_HT_INT: BRANCH(int32_t,ptr[l_ori]==bcf_int32_vector_end); break;
case BCF_HT_REAL: BRANCH(float,bcf_float_is_vector_end(ptr[l_ori])); break;
}
#undef BRANCH
}
nret = bcf_update_info(header, line, bcf_hdr_int2id(header,BCF_DT_ID,info->key), (void*)dat, ndat, type);
if ( nret<0 )
{
fprintf(stderr,"[%s:%d %s] Could not update INFO/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__,
bcf_hdr_int2id(header,BCF_DT_ID,info->key), bcf_seqname(header,line), line->pos+1, nret);
exit(1);
}
}
// Update GT fields, the allele indexes might have changed
for (i=1; i<line->n_allele; i++) if ( map[i]!=i ) break;
if ( i<line->n_allele )
{
mdat = mdat_bytes / 4; // sizeof(int32_t)
nret = bcf_get_genotypes(header,line,(void**)&dat,&mdat);
mdat_bytes = mdat * 4;
if ( nret>0 )
{
nret /= line->n_sample;
int32_t *ptr = (int32_t*) dat;
for (i=0; i<line->n_sample; i++)
{
for (j=0; j<nret; j++)
{
if ( ptr[j]==bcf_gt_missing ) continue;
if ( ptr[j]==bcf_int32_vector_end ) break;
int al = bcf_gt_allele(ptr[j]);
assert( al<nR_ori && map[al]>=0 );
ptr[j] = (map[al]+1)<<1 | (ptr[j]&1);
}
ptr += nret;
}
bcf_update_genotypes(header, line, (void*)dat, nret*line->n_sample);
}
}
// Remove from Number=G, Number=R and Number=A FORMAT fields.
// Assuming haploid or diploid GTs
for (i=0; i<line->n_fmt; i++)
{
bcf_fmt_t *fmt = &line->d.fmt[i];
int vlen = bcf_hdr_id2length(header,BCF_HL_FMT,fmt->id);
if ( vlen!=BCF_VL_A && vlen!=BCF_VL_G && vlen!=BCF_VL_R ) continue; // no need to change
int type = bcf_hdr_id2type(header,BCF_HL_FMT,fmt->id);
if ( type==BCF_HT_FLAG ) continue;
int size = 1;
if ( type==BCF_HT_REAL || type==BCF_HT_INT ) size = 4;
mdat = mdat_bytes / size;
nret = bcf_get_format_values(header, line, bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), (void**)&dat, &mdat, type);
mdat_bytes = mdat * size;
if ( nret<0 )
{
fprintf(stderr,"[%s:%d %s] Could not access FORMAT/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__,
bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), bcf_seqname(header,line), line->pos+1, nret);
exit(1);
}
if ( type==BCF_HT_STR )
{
int size = nret/line->n_sample; // number of bytes per sample
str.l = 0;
if ( vlen==BCF_VL_A || vlen==BCF_VL_R )
{
int nexp, inc = 0;
if ( vlen==BCF_VL_A )
{
nexp = nA_ori;
inc = 1;
}
else
nexp = nR_ori;
for (j=0; j<line->n_sample; j++)
{
char *ss = ((char*)dat) + j*size, *se = ss + size, *ptr = ss;
int k_src = 0, k_dst = 0, l = str.l;
for (k_src=0; k_src<nexp; k_src++)
{
if ( ptr>=se || !*ptr) break;
while ( ptr<se && *ptr && *ptr!=',' ) ptr++;
if ( rm_mask & 1<<(k_src+inc) )
{
ss = ++ptr;
continue;
}
if ( k_dst ) kputc(',',&str);
kputsn(ss,ptr-ss,&str);
ss = ++ptr;
k_dst++;
}
assert( k_src==nexp );
l = str.l - l;
for (; l<size; l++) kputc(0, &str);
}
}
else // Number=G, diploid or haploid
{
for (j=0; j<line->n_sample; j++)
{
char *ss = ((char*)dat) + j*size, *se = ss + size, *ptr = ss;
int k_src = 0, k_dst = 0, l = str.l;
int nexp = 0; // diploid or haploid?
while ( ptr<se )
{
if ( !*ptr ) break;
if ( *ptr==',' ) nexp++;
ptr++;
}
if ( ptr!=ss ) nexp++;
assert( nexp==nG_ori || nexp==nR_ori );
ptr = ss;
if ( nexp==nG_ori ) // diploid
{
int ia, ib;
for (ia=0; ia<nR_ori; ia++)
{
for (ib=0; ib<=ia; ib++)
{
if ( ptr>=se || !*ptr ) break;
while ( ptr<se && *ptr && *ptr!=',' ) ptr++;
if ( rm_mask & 1<<ia || rm_mask & 1<<ib )
{
ss = ++ptr;
continue;
}
if ( k_dst ) kputc(',',&str);
kputsn(ss,ptr-ss,&str);
ss = ++ptr;
k_dst++;
}
if ( ptr>=se || !*ptr ) break;
}
}
else // haploid
{
for (k_src=0; k_src<nR_ori; k_src++)
{
if ( ptr>=se || !*ptr ) break;
while ( ptr<se && *ptr && *ptr!=',' ) ptr++;
if ( rm_mask & 1<<k_src )
{
ss = ++ptr;
continue;
}
if ( k_dst ) kputc(',',&str);
kputsn(ss,ptr-ss,&str);
ss = ++ptr;
k_dst++;
}
assert( k_src==nR_ori );
l = str.l - l;
for (; l<size; l++) kputc(0, &str);
}
}
}
nret = bcf_update_format(header, line, bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), (void*)str.s, str.l, type);
if ( nret<0 )
{
fprintf(stderr,"[%s:%d %s] Could not update FORMAT/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__,
bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), bcf_seqname(header,line), line->pos+1, nret);
exit(1);
}
continue;
}
int nori = nret / line->n_sample;
if ( vlen==BCF_VL_A || vlen==BCF_VL_R || (vlen==BCF_VL_G && nori==nR_ori) ) // Number=A, R or haploid Number=G
{
int ntop, inc = 0;
if ( vlen==BCF_VL_A )
{
assert( nori==nA_ori ); // todo: will fail if all values are missing
ntop = nA_ori;
ndat = nA_new*line->n_sample;
inc = 1;
}
else
{
assert( nori==nR_ori ); // todo: will fail if all values are missing
ntop = nR_ori;
ndat = nR_new*line->n_sample;
}
#define BRANCH(type_t,is_vector_end) \
{ \
for (j=0; j<line->n_sample; j++) \
{ \
type_t *ptr_src = ((type_t*)dat) + j*nori; \
type_t *ptr_dst = ((type_t*)dat) + j*nA_new; \
int size = sizeof(type_t); \
int k_src, k_dst = 0; \
for (k_src=0; k_src<ntop; k_src++) \
{ \
if ( is_vector_end ) { memcpy(ptr_dst+k_dst, ptr_src+k_src, size); break; } \
if ( rm_mask & 1<<(k_src+inc) ) continue; \
if ( k_src!=k_dst ) memcpy(ptr_dst+k_dst, ptr_src+k_src, size); \
k_dst++; \
} \
} \
}
switch (type)
{
case BCF_HT_INT: BRANCH(int32_t,ptr_src[k_src]==bcf_int32_vector_end); break;
case BCF_HT_REAL: BRANCH(float,bcf_float_is_vector_end(ptr_src[k_src])); break;
}
#undef BRANCH
}
else // Number=G, diploid or mixture of haploid+diploid
{
assert( nori==nG_ori );
ndat = nG_new*line->n_sample;
#define BRANCH(type_t,is_vector_end) \
{ \
for (j=0; j<line->n_sample; j++) \
{ \
type_t *ptr_src = ((type_t*)dat) + j*nori; \
type_t *ptr_dst = ((type_t*)dat) + j*nG_new; \
int size = sizeof(type_t); \
int ia, ib, k_dst = 0, k_src; \
int nset = 0; /* haploid or diploid? */ \
for (k_src=0; k_src<nG_ori; k_src++) { if ( is_vector_end ) break; nset++; } \
if ( nset==nR_ori ) /* haploid */ \
{ \
for (k_src=0; k_src<nR_ori; k_src++) \
{ \
if ( rm_mask & 1<<k_src ) continue; \
if ( k_src!=k_dst ) memcpy(ptr_dst+k_dst, ptr_src+k_src, size); \
k_dst++; \
} \
memcpy(ptr_dst+k_dst, ptr_src+k_src, size); \
} \
else /* diploid */ \
{ \
k_src = -1; \
for (ia=0; ia<nR_ori; ia++) \
{ \
for (ib=0; ib<=ia; ib++) \
{ \
k_src++; \
if ( is_vector_end ) { memcpy(ptr_dst+k_dst, ptr_src+k_src, size); ia = nR_ori; break; } \
if ( rm_mask & 1<<ia || rm_mask & 1<<ib ) continue; \
if ( k_src!=k_dst ) memcpy(ptr_dst+k_dst, ptr_src+k_src, size); \
k_dst++; \
} \
} \
} \
} \
}
switch (type)
{
case BCF_HT_INT: BRANCH(int32_t,ptr_src[k_src]==bcf_int32_vector_end); break;
case BCF_HT_REAL: BRANCH(float,bcf_float_is_vector_end(ptr_src[k_src])); break;
}
#undef BRANCH
}
nret = bcf_update_format(header, line, bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), (void*)dat, ndat, type);
if ( nret<0 )
{
fprintf(stderr,"[%s:%d %s] Could not update FORMAT/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__,
bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), bcf_seqname(header,line), line->pos+1, nret);
exit(1);
}
}
free(dat);
free(str.s);
free(map);
}
bcf1_t *process(bcf1_t *rec)
{
bcf1_t *dflt = args.mode&MODE_LIST_GOOD ? rec : NULL;
args.nrec++;
if ( rec->n_allele > 63 ) return dflt; // we use 64bit bitmask below
int ngt = bcf_get_genotypes(args.hdr, rec, &args.gt_arr, &args.ngt_arr);
if ( ngt<0 ) return dflt;
if ( ngt!=2*bcf_hdr_nsamples(args.hdr) && ngt!=bcf_hdr_nsamples(args.hdr) ) return dflt;
ngt /= bcf_hdr_nsamples(args.hdr);
int itr_set = regidx_overlap(args.rules, bcf_seqname(args.hdr,rec),rec->pos,rec->pos, args.itr_ori);
int i, has_bad = 0, needs_update = 0;
for (i=0; i<args.ntrios; i++)
{
int32_t a,b,c,d,e,f;
trio_t *trio = &args.trios[i];
a = args.gt_arr[ngt*trio->imother];
b = ngt==2 ? args.gt_arr[ngt*trio->imother+1] : bcf_int32_vector_end;
c = args.gt_arr[ngt*trio->ifather];
d = ngt==2 ? args.gt_arr[ngt*trio->ifather+1] : bcf_int32_vector_end;
e = args.gt_arr[ngt*trio->ichild];
f = ngt==2 ? args.gt_arr[ngt*trio->ichild+1] : bcf_int32_vector_end;
// skip sites with missing data in child
if ( bcf_gt_is_missing(e) || bcf_gt_is_missing(f) ) continue;
uint64_t mother = 0, father = 0,child1,child2;
int is_ok = 0;
if ( !itr_set )
{
if ( f==bcf_int32_vector_end ) { warn_ploidy(rec); continue; }
// All M,F,C genotypes are diploid. Missing data are considered consistent.
child1 = 1<<bcf_gt_allele(e);
child2 = 1<<bcf_gt_allele(f);
mother = bcf_gt_is_missing(a) ? child1|child2 : 1<<bcf_gt_allele(a);
mother |= bcf_gt_is_missing(b) || b==bcf_int32_vector_end ? child1|child2 : 1<<bcf_gt_allele(b);
father = bcf_gt_is_missing(c) ? child1|child2 : 1<<bcf_gt_allele(c);
father |= bcf_gt_is_missing(d) || d==bcf_int32_vector_end ? child1|child2 : 1<<bcf_gt_allele(d);
if ( (mother&child1 && father&child2) || (mother&child2 && father&child1) ) is_ok = 1;
}
else
{
child1 = 1<<bcf_gt_allele(e);
child2 = bcf_gt_is_missing(f) || f==bcf_int32_vector_end ? 0 : 1<<bcf_gt_allele(f);
mother |= bcf_gt_is_missing(a) ? 0 : 1<<bcf_gt_allele(a);
mother |= bcf_gt_is_missing(b) || b==bcf_int32_vector_end ? 0 : 1<<bcf_gt_allele(b);
father |= bcf_gt_is_missing(c) ? 0 : 1<<bcf_gt_allele(c);
father |= bcf_gt_is_missing(d) || d==bcf_int32_vector_end ? 0 : 1<<bcf_gt_allele(d);
regitr_copy(args.itr, args.itr_ori);
while ( !is_ok && regitr_overlap(args.itr) )
{
rule_t *rule = ®itr_payload(args.itr,rule_t);
if ( child1 && child2 )
{
if ( !rule->mal || !rule->fal ) continue; // wrong rule (haploid), but this is a diploid GT
if ( !mother ) mother = child1|child2;
if ( !father ) father = child1|child2;
if ( (mother&child1 && father&child2) || (mother&child2 && father&child1) ) is_ok = 1;
continue;
}
if ( rule->mal )
{
if ( mother && !(child1&mother) ) continue;
}
if ( rule->fal )
{
if ( father && !(child1&father) ) continue;
}
is_ok = 1;
}
}
if ( is_ok )
{
trio->nok++;
}
else
{
trio->nbad++;
has_bad = 1;
if ( args.mode&MODE_DELETE )
{
args.gt_arr[ngt*trio->imother] = bcf_gt_missing;
if ( b!=bcf_int32_vector_end ) args.gt_arr[ngt*trio->imother+1] = bcf_gt_missing; // should be always true
args.gt_arr[ngt*trio->ifather] = bcf_gt_missing;
if ( d!=bcf_int32_vector_end ) args.gt_arr[ngt*trio->ifather+1] = bcf_gt_missing;
args.gt_arr[ngt*trio->ichild] = bcf_gt_missing;
if ( f!=bcf_int32_vector_end ) args.gt_arr[ngt*trio->ichild+1] = bcf_gt_missing;
needs_update = 1;
}
}
}
if ( needs_update && bcf_update_genotypes(args.hdr,rec,args.gt_arr,ngt*bcf_hdr_nsamples(args.hdr)) )
error("Could not update GT field at %s:%d\n", bcf_seqname(args.hdr,rec),rec->pos+1);
if ( args.mode&MODE_DELETE ) return rec;
if ( args.mode&MODE_LIST_GOOD ) return has_bad ? NULL : rec;
if ( args.mode&MODE_LIST_BAD ) return has_bad ? rec : NULL;
return NULL;
}
void abcWriteBcf::print(funkyPars *pars){
if(doBcf==0)
return;
kstring_t buf;
if(fp==NULL){
buf.s=NULL;buf.l=buf.m=0;
fp=aio::openFileHts(outfiles,".bcf");
hdr = bcf_hdr_init("w");
rec = bcf_init1();
print_bcf_header(fp,hdr,args,buf,header);
}
lh3struct *lh3 = (lh3struct*) pars->extras[5];
freqStruct *freq = (freqStruct *) pars->extras[6];
genoCalls *geno = (genoCalls *) pars->extras[10];
for(int s=0;s<pars->numSites;s++){
if(pars->keepSites[s]==0)
continue;
rec->rid = bcf_hdr_name2id(hdr,header->target_name[pars->refId]);
rec->pos = pars->posi[s];//<- maybe one index?
// bcf_update_id(hdr, rec, "rs6054257");
char majmin[4]={intToRef[pars->major[s]],',',intToRef[pars->minor[s]],'\0'};
bcf_update_alleles_str(hdr, rec, majmin);
rec->qual = 29;
// .. FILTER
int32_t tmpi = bcf_hdr_id2int(hdr, BCF_DT_ID, "PASS");
bcf_update_filter(hdr, rec, &tmpi, 1);
// .. INFO
tmpi = pars->keepSites[s];
bcf_update_info_int32(hdr, rec, "NS", &tmpi, 1);
if(pars->counts){
int depth = 0;
for(int i=0; i<4*pars->nInd; i++)
depth += pars->counts[s][i];
tmpi = depth;
bcf_update_info_int32(hdr, rec, "DP", &tmpi, 1);
}
if(freq){
float tmpf = freq->freq_EM[s];
bcf_update_info_float(hdr, rec, "AF", &tmpf, 1);
}
// .. FORMAT
assert(geno);
if(geno){
int32_t *tmpia = (int*)malloc(bcf_hdr_nsamples(hdr)*2*sizeof(int32_t));
for(int i=0; i<pars->nInd;i++){
if(geno->dat[s][i]==0){
tmpia[2*i+0] = bcf_gt_unphased(0);
tmpia[2*i+1] = bcf_gt_unphased(0);
}else if(geno->dat[s][i]==1){
tmpia[2*i+0] = bcf_gt_unphased(0);
tmpia[2*i+1] = bcf_gt_unphased(1);
} else{
tmpia[2*i+0] = bcf_gt_unphased(1);
tmpia[2*i+1] = bcf_gt_unphased(1);
}
}
bcf_update_genotypes(hdr, rec, tmpia, bcf_hdr_nsamples(hdr)*2);
free(tmpia);
}
if(pars->counts){
int32_t *tmpfa = (int32_t*)malloc(sizeof(int32_t)*bcf_hdr_nsamples(hdr));
suint *ary=pars->counts[s];
for(int i=0;i<bcf_hdr_nsamples(hdr);i++)
tmpfa[i] = ary[0]+ary[1]+ary[2]+ary[3];
bcf_update_format_int32(hdr, rec, "DP", tmpfa,bcf_hdr_nsamples(hdr) );
free(tmpfa);
}
assert(lh3);
if(lh3){
float *tmpfa = (float*)malloc(3*bcf_hdr_nsamples(hdr)*sizeof(float ));
int32_t *tmpi = (int32_t*)malloc(3*bcf_hdr_nsamples(hdr)*sizeof(int32_t));
double *ary = lh3->lh3[s];
for(int i=0;i<bcf_hdr_nsamples(hdr);i++)
for(int j=0;j<3;j++){
tmpfa[i*3+j] = ary[i*3+j]/M_LN10;
tmpi[i*3+j] =(int) -log10(exp(ary[i*3+j]))*10.0;
// fprintf(stderr,"pl:%d raw:%f\n",tmpi[i*3+j],ary[i*3+j]);
}
bcf_update_format_float(hdr, rec, "GL", tmpfa,3*bcf_hdr_nsamples(hdr) );
bcf_update_format_int32(hdr, rec, "PL", tmpi,3*bcf_hdr_nsamples(hdr) );
free(tmpfa);
free(tmpi);
}
if ( bcf_write1(fp, hdr, rec)!=0 ){
fprintf(stderr,"Failed to write to \n");
exit(0);
}
// fprintf(stderr,"------\n");
bcf_clear1(rec);
}
}
