/**
* Updates a bcf1_t object with VNTR information.
*/
void Variant::update_bcf_with_vntr_info(bcf_hdr_t *h, bcf1_t *v)
{
bcf_update_info_flag(h, v, "FUZZY", NULL, 1);
//VNTR position and sequences
bcf_set_pos1(v, vntr.fuzzy_beg1);
kstring_t s = {0,0,0};
s.l = 0;
kputs(vntr.fuzzy_repeat_tract.c_str(), &s);
kputc(',', &s);
kputs("<VNTR>", &s);
bcf_update_alleles_str(h, v, s.s);
//VNTR motif
bcf_update_info_string(h, v, "MOTIF", vntr.motif.c_str());
bcf_update_info_string(h, v, "RU", vntr.ru.c_str());
//VNTR characteristics
bcf_update_info_float(h, v, "FZ_CONCORDANCE", &vntr.fuzzy_score, 1);
bcf_update_info_float(h, v, "FZ_RL", &vntr.fuzzy_rl, 1);
bcf_update_info_float(h, v, "FZ_LL", &vntr.fuzzy_ll, 1);
int32_t flank_pos1[2] = {vntr.exact_beg1-1, vntr.exact_end1+1};
bcf_update_info_int32(h, v, "FLANKS", &flank_pos1, 2);
//flank positions
int32_t fuzzy_flank_pos1[2] = {vntr.fuzzy_beg1-1, vntr.fuzzy_end1+1};
bcf_update_info_int32(h, v, "FZ_FLANKS", &fuzzy_flank_pos1, 2);
int32_t ru_count[2] = {vntr.fuzzy_no_perfect_ru, vntr.fuzzy_no_ru};
bcf_update_info_int32(h, v, "FZ_RU_COUNTS", &ru_count, 2);
if (vntr.is_large_repeat_tract) bcf_update_info_flag(h, v, "LARGE_REPEAT_REGION", NULL, 1);
if (s.m) free(s.s);
}
bcf1_t *process(bcf1_t *rec)
{
int nval = 0, i, j, nret = bcf_get_format_values(in_hdr,rec,"GP",(void**)&buf,&nbuf,gp_type);
if ( nret<0 )
{
if (!nskip_gp) fprintf(stderr, "[impute-info.c] Warning: info tag not added to sites without GP tag\n");
nskip_gp++;
return rec; // require FORMAT/GP tag, return site unchanged
}
nret /= rec->n_sample;
if ( nret != 3 )
{
if (!nskip_dip) fprintf(stderr, "[impute-info.c] Warning: info tag not added to sites that are not biallelic diploid\n");
nskip_dip++;
return rec; // require biallelic diploid, return site unchanged
}
double esum = 0, e2sum = 0, fsum = 0;
#define BRANCH(type_t,is_missing,is_vector_end) \
{ \
type_t *ptr = (type_t*) buf; \
for (i=0; i<rec->n_sample; i++) \
{ \
double vals[3] = {0,0,0}; \
for (j=0; j<nret; j++) \
{ \
if ( is_missing || is_vector_end ) break; \
vals[j] = ptr[j]; \
} \
esum += vals[1] + 2*vals[2]; \
e2sum += (vals[1] + 2*vals[2]) * (vals[1] + 2*vals[2]); \
fsum += vals[1] + 4*vals[2]; \
ptr += nret; \
nval++; \
} \
}
switch (gp_type)
{
case BCF_HT_INT: BRANCH(int32_t,ptr[j]==bcf_int32_missing,ptr[j]==bcf_int32_vector_end); break;
case BCF_HT_REAL: BRANCH(float,bcf_float_is_missing(ptr[j]),bcf_float_is_vector_end(ptr[j])); break;
}
#undef BRANCH
double theta = esum / (2 * (double)nval);
float info = (theta>0 && theta<1) ? (float)(1 - (fsum - e2sum) / (2 * (double)nval * theta * (1.0 - theta))) : 1;
bcf_update_info_float(out_hdr, rec, "INFO", &info, 1);
nrec++;
return rec;
}
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;
}
static int update_bcf1(call_t *call, bcf1_t *rec, const bcf_p1rst_t *pr, double em[10])
{
int has_I16, is_var;
float fq, r;
anno16_t a;
float tmpf[4], tmpi;
bcf_get_info_float(call->hdr, rec, "I16", &call->anno16, &call->n16);
has_I16 = test16(call->anno16, &a) >= 0? 1 : 0;
// print EM
if (em[0] >= 0)
{
tmpf[0] = 1 - em[0];
bcf_update_info_float(call->hdr, rec, "AF1", tmpf, 1);
}
if (em[4] >= 0 && em[4] <= 0.05)
{
tmpf[0] = em[3]; tmpf[1] = em[2]; tmpf[2] = em[1]; tmpf[3] = em[4];
bcf_update_info_float(call->hdr, rec, "G3", tmpf, 3);
bcf_update_info_float(call->hdr, rec, "HWE", &tmpf[3], 1);
}
if (em[5] >= 0 && em[6] >= 0)
{
tmpf[0] = 1 - em[5]; tmpf[1] = 1 - em[6];
bcf_update_info_float(call->hdr, rec, "AF2", tmpf, 2);
}
if (em[7] >= 0)
{
tmpf[0] = em[7];
bcf_update_info_float(call->hdr, rec, "LRT", tmpf, 1);
}
if (em[8] >= 0)
{
tmpf[0] = em[8];
bcf_update_info_float(call->hdr, rec, "LRT2", tmpf, 1);
}
bcf_p1aux_t *p1 = call->cdat->p1;
if (p1->cons_llr > 0)
{
tmpi = p1->cons_llr;
bcf_update_info_int32(call->hdr, rec, "CLR", &tmpi, 1);
// todo: trio calling with -c
if (p1->cons_gt > 0)
{
char tmp[4];
tmp[0] = p1->cons_gt&0xff; tmp[1] = p1->cons_gt>>8&0xff; tmp[2] = p1->cons_gt>>16&0xff; tmp[3] = 0;
bcf_update_info_string(call->hdr, rec, "UGT", tmp);
tmp[0] = p1->cons_gt>>32&0xff; tmp[1] = p1->cons_gt>>40&0xff; tmp[2] = p1->cons_gt>>48&0xff;
bcf_update_info_string(call->hdr, rec, "CGT", tmp);
}
//{{{ void print_query_result_offset(uint32_t *mask,
void print_query_result_offset(uint32_t *mask,
uint32_t mask_len,
uint32_t *vids,
struct gqt_query *q,
uint32_t **counts,
uint32_t *id_lens,
uint32_t *U_R,
uint32_t U_R_len,
char **id_query_list,
char **gt_query_list,
uint32_t num_qs,
uint32_t num_fields,
char *off_file_name,
char *source_file,
char *full_cmd)
{
struct off_file *off_f = open_off_file(off_file_name);
struct bcf_file bcf_f = init_bcf_file(source_file);
char *sample_names = NULL;
uint32_t i,j,k,line_idx,bytes, bit_i = 0;
int r;
for (i = 0; i < U_R_len; ++i) {
if (i == 0 )
r = asprintf(&sample_names,
"%s",
bcf_f.hdr->samples[U_R[i]]);
else
r = asprintf(&sample_names,
"%s,%s",
sample_names,
bcf_f.hdr->samples[U_R[i]]);
if (r == -1)
err(EX_OSERR, "asprintf error");
}
if (bcf_hdr_set_samples(bcf_f.hdr, sample_names, 0) != 0)
errx(EX_DATAERR, "Error setting samples: %s\n", source_file);
char *info_s;
for (i = 0; i < num_qs; i++) {
if ( q[i].variant_op == p_count ) {
r = asprintf(&info_s, "##INFO=<ID=GQT_%u,Number=1,Type=Integer,"
"Description=\"GQT count result from "
"phenotype:'%s' genotype:'%s'\">",
i, id_query_list[i], gt_query_list[i]);
if (r == -1) err(EX_OSERR, "asprintf error");
if (bcf_hdr_append(bcf_f.hdr, info_s) != 0)
errx(EX_DATAERR, "Error updating header: %s\n", source_file);
} else if ( q[i].variant_op == p_pct ) {
r = asprintf(&info_s, "##INFO=<ID=GQT_%u,Number=1,Type=Float,"
"Description=\"GQT percent result from "
"phenotype:'%s' genotype:'%s'\">",
i, id_query_list[i], gt_query_list[i]);
if (r == -1) err(EX_OSERR, "asprintf error");
if (bcf_hdr_append(bcf_f.hdr, info_s) != 0)
errx(EX_DATAERR, "Error updating header: %s\n", source_file);
} else if ( q[i].variant_op == p_maf ) {
r = asprintf(&info_s, "##INFO=<ID=GQT_%u,Number=1,Type=Float,"
"Description=\"GQT maf result from "
"phenotype:'%s' genotype:'%s'\">",
i, id_query_list[i], gt_query_list[i]);
if (bcf_hdr_append(bcf_f.hdr, info_s) != 0)
errx(EX_DATAERR, "Error updating header: %s\n", source_file);
}
}
r = asprintf(&info_s, "##%s_queryVersion=%s", PROGRAM_NAME, VERSION);
if (r == -1) err(EX_OSERR, "asprintf error");
if (bcf_hdr_append(bcf_f.hdr, info_s) != 0)
errx(EX_DATAERR, "Error updating header: %s\n", source_file);
r = asprintf(&info_s, "##%s_queryCommand=%s", PROGRAM_NAME, full_cmd);
if (r == -1) err(EX_OSERR, "asprintf error");
if (bcf_hdr_append(bcf_f.hdr, info_s) != 0)
errx(EX_DATAERR, "Error updating header: %s\n", source_file);
htsFile *out_f = hts_open("-","w");
if ( !out_f )
err(EX_DATAERR, "Could open output file");
bcf_hdr_write(out_f, bcf_f.hdr);
bcf_f.line = bcf_init1();
for (i=0; i < mask_len; ++i) {
bytes = mask[i];
if (bytes == 0)
continue; /* skip a bunch of ops if you can */
for (j=0; j < 32; j++) {
if (bytes & 1 << (31 - j)) {
line_idx = i*32+j;
r = goto_bcf_line(&bcf_f, off_f, line_idx);
if (r == -1)
err(EX_NOINPUT,
"Error seeking file '%s'", bcf_f.file_name);
r = get_bcf_line(&bcf_f);
if (r == -1)
err(EX_NOINPUT,
"Error reading file '%s'", bcf_f.file_name);
for (k=0; k < num_qs; k++) {
r = asprintf(&info_s, "GQT_%u", k);
if (r == -1)
err(EX_OSERR, "asprintf error");
if ( q[k].variant_op == p_count ) {
int32_t v = counts[k][line_idx];
if (bcf_update_info_int32(bcf_f.hdr,
bcf_f.line,
info_s,
&v,
1) != 0)
errx(EX_DATAERR,
"Error adding to info field: %s\n",
bcf_f.file_name);
} else if (q[k].variant_op == p_pct) {
float v = ((float)counts[k][line_idx])/
((float) id_lens[k]);
if (bcf_update_info_float(bcf_f.hdr,
bcf_f.line,
info_s,
&v,
1) != 0)
errx(EX_DATAERR,
"Error adding to info field: %s\n",
bcf_f.file_name);
} else if (q[k].variant_op == p_maf) {
float v = ((float)counts[k][line_idx])/
(((float) id_lens[k])*2.0);
if (bcf_update_info_float(bcf_f.hdr,
bcf_f.line,
info_s,
&v,
1) != 0)
errx(EX_DATAERR,
"Error adding to info field: %s\n",
bcf_f.file_name);
}
}
bcf_write(out_f, bcf_f.hdr, bcf_f.line);
}
bit_i++;
if (bit_i == num_fields)
break;
}
if (bit_i == num_fields)
break;
}
hts_close(out_f);
destroy_off_file(off_f);
}
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);
}
}
bcf1_t *process(bcf1_t *rec)
{
int i, ns = 0;
bcf_unpack(rec, BCF_UN_FMT);
bcf_fmt_t *fmt_gt = NULL;
for (i=0; i<rec->n_fmt; i++)
if ( rec->d.fmt[i].id==args.gt_id ) { fmt_gt = &rec->d.fmt[i]; break; }
if ( !fmt_gt ) return rec; // no GT tag
hts_expand(int32_t,rec->n_allele,args.marr,args.arr);
hts_expand(float,rec->n_allele,args.mfarr,args.farr);
hts_expand(counts_t,rec->n_allele,args.mcounts,args.counts);
memset(args.arr,0,sizeof(*args.arr)*rec->n_allele);
memset(args.counts,0,sizeof(*args.counts)*rec->n_allele);
#define BRANCH_INT(type_t,vector_end) { \
for (i=0; i<rec->n_sample; i++) \
{ \
type_t *p = (type_t*) (fmt_gt->p + i*fmt_gt->size); \
int ial, als = 0; \
for (ial=0; ial<fmt_gt->n; ial++) \
{ \
if ( p[ial]==vector_end ) break; /* smaller ploidy */ \
if ( bcf_gt_is_missing(p[ial]) ) break; /* missing allele */ \
int idx = bcf_gt_allele(p[ial]); \
\
if ( idx >= rec->n_allele ) \
error("Incorrect allele (\"%d\") in %s at %s:%d\n",idx,args.in_hdr->samples[i],bcf_seqname(args.in_hdr,rec),rec->pos+1); \
als |= (1<<idx); /* this breaks with too many alleles */ \
} \
if ( ial==0 ) continue; /* missing alleles */ \
ns++; \
int is_hom = als && !(als & (als-1)); /* only one bit is set */ \
int is_hemi = ial==1; \
for (ial=0; als; ial++) \
{ \
if ( als&1 ) \
{ \
if ( !is_hom ) \
args.counts[ial].nhet++; \
else if ( !is_hemi ) \
args.counts[ial].nhom += 2; \
else \
args.counts[ial].nhemi++; \
} \
als >>= 1; \
} \
} \
}
switch (fmt_gt->type) {
case BCF_BT_INT8: BRANCH_INT(int8_t, bcf_int8_vector_end); break;
case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_vector_end); break;
case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_vector_end); break;
default: error("The GT type is not recognised: %d at %s:%d\n",fmt_gt->type, bcf_seqname(args.in_hdr,rec),rec->pos+1); break;
}
#undef BRANCH_INT
if ( args.tags&SET_NS )
{
if ( bcf_update_info_int32(args.out_hdr,rec,"NS",&ns,1)!=0 )
error("Error occurred while updating NS at %s:%d\n", bcf_seqname(args.in_hdr,rec),rec->pos+1);
}
if ( args.tags&SET_AN )
{
args.arr[0] = 0;
for (i=0; i<rec->n_allele; i++)
args.arr[0] += args.counts[i].nhet + args.counts[i].nhom + args.counts[i].nhemi;
if ( bcf_update_info_int32(args.out_hdr,rec,"AN",args.arr,1)!=0 )
error("Error occurred while updating AN at %s:%d\n", bcf_seqname(args.in_hdr,rec),rec->pos+1);
}
if ( args.tags&SET_AF )
{
int n = rec->n_allele-1;
if ( n>0 )
{
args.arr[0] = 0;
for (i=0; i<rec->n_allele; i++)
args.arr[0] += args.counts[i].nhet + args.counts[i].nhom + args.counts[i].nhemi;
for (i=1; i<rec->n_allele; i++)
args.farr[i] = (args.counts[i].nhet + args.counts[i].nhom + args.counts[i].nhemi)*1.0/args.arr[0];
}
if ( args.arr[0] )
{
if ( bcf_update_info_float(args.out_hdr,rec,"AF",args.farr+1,n)!=0 )
error("Error occurred while updating AF at %s:%d\n", bcf_seqname(args.in_hdr,rec),rec->pos+1);
}
}
if ( args.tags&SET_AC )
{
int n = rec->n_allele-1;
if ( n>0 )
{
memset(args.arr,0,sizeof(*args.arr)*rec->n_allele);
for (i=1; i<rec->n_allele; i++)
args.arr[i] = args.counts[i].nhet + args.counts[i].nhom + args.counts[i].nhemi;
}
if ( bcf_update_info_int32(args.out_hdr,rec,"AC",args.arr+1,n)!=0 )
error("Error occurred while updating AC at %s:%d\n", bcf_seqname(args.in_hdr,rec),rec->pos+1);
}
if ( args.tags&SET_AC_Het )
{
int n = rec->n_allele-1;
if ( n>0 )
{
memset(args.arr,0,sizeof(*args.arr)*rec->n_allele);
for (i=1; i<rec->n_allele; i++)
args.arr[i] += args.counts[i].nhet;
}
if ( bcf_update_info_int32(args.out_hdr,rec,"AC_Het",args.arr+1,n)!=0 )
error("Error occurred while updating AC_Het at %s:%d\n", bcf_seqname(args.in_hdr,rec),rec->pos+1);
}
if ( args.tags&SET_AC_Hom )
{
int n = rec->n_allele-1;
if ( n>0 )
{
memset(args.arr,0,sizeof(*args.arr)*rec->n_allele);
for (i=1; i<rec->n_allele; i++)
args.arr[i] += args.counts[i].nhom;
}
if ( bcf_update_info_int32(args.out_hdr,rec,"AC_Hom",args.arr+1,n)!=0 )
error("Error occurred while updating AC_Hom at %s:%d\n", bcf_seqname(args.in_hdr,rec),rec->pos+1);
}
if ( args.tags&SET_AC_Hemi )
{
int n = rec->n_allele-1;
if ( n>0 )
{
memset(args.arr,0,sizeof(*args.arr)*rec->n_allele);
for (i=1; i<rec->n_allele; i++)
args.arr[i] += args.counts[i].nhemi;
}
if ( bcf_update_info_int32(args.out_hdr,rec,"AC_Hemi",args.arr+1,n)!=0 )
error("Error occurred while updating AC_Hemi at %s:%d\n", bcf_seqname(args.in_hdr,rec),rec->pos+1);
}
return rec;
}
