static bcf_hdr_t *strip_header(bcf_hdr_t *src, bcf_hdr_t *dst)
{
bcf_hrec_t *src_hrec, *dst_hrec, *tmp;
bcf_hdr_t *out = bcf_hdr_init("r");
int i;
for (i=0; i<dst->nhrec; i++)
{
// first insert lines which do not code BCF ids, their order does not matter
dst_hrec = dst->hrec[i];
if ( dst_hrec->type==BCF_HL_FLT || dst_hrec->type==BCF_HL_INFO || dst_hrec->type==BCF_HL_FMT || dst_hrec->type== BCF_HL_CTG ) continue;
bcf_hdr_add_hrec(out, bcf_hrec_dup(dst_hrec));
}
for (i=0; i<src->nhrec; i++)
{
// now transfer header lines which define BCF ids
src_hrec = src->hrec[i];
if ( src_hrec->type==BCF_HL_FLT || src_hrec->type==BCF_HL_INFO || src_hrec->type==BCF_HL_FMT || src_hrec->type== BCF_HL_CTG )
{
int j = bcf_hrec_find_key(src_hrec, "ID");
dst_hrec = bcf_hdr_get_hrec(dst, src_hrec->type, "ID", src_hrec->vals[j], NULL);
if ( !dst_hrec ) continue;
tmp = bcf_hrec_dup(dst_hrec);
j = bcf_hrec_find_key(src_hrec, "IDX");
if ( j>=0 )
{
j = atoi(src_hrec->vals[j]);
hrec_add_idx(tmp, j);
}
bcf_hdr_add_hrec(out, tmp);
}
}
bcf_hdr_sync(out);
for (i=0; i<dst->nhrec; i++)
{
// finally add new structured fields
dst_hrec = dst->hrec[i];
if ( dst_hrec->type==BCF_HL_FLT || dst_hrec->type==BCF_HL_INFO || dst_hrec->type==BCF_HL_FMT || dst_hrec->type== BCF_HL_CTG )
{
int j = bcf_hrec_find_key(dst_hrec, "ID");
tmp = bcf_hdr_get_hrec(out, dst_hrec->type, "ID", dst_hrec->vals[j], NULL);
if ( !tmp )
bcf_hdr_add_hrec(out, bcf_hrec_dup(dst_hrec));
}
}
for (i=0; i<dst->n[BCF_DT_SAMPLE]; i++) bcf_hdr_add_sample(out, dst->samples[i]);
bcf_hdr_add_sample(out, NULL);
bcf_hdr_destroy(dst);
return out;
}
void bcf_hdr_merge(bcf_hdr_t *hw, const bcf_hdr_t *_hr, const char *clash_prefix)
{
bcf_hdr_t *hr = (bcf_hdr_t*)_hr;
// header lines
int i, nw_ori = hw->nhrec;
for (i=0; i<hr->nhrec; i++)
{
if ( hr->hrec[i]->type==BCF_HL_GEN && hr->hrec[i]->value )
{
int j;
for (j=0; j<nw_ori; j++)
{
if ( hw->hrec[j]->type!=BCF_HL_GEN ) continue;
if ( !strcmp(hr->hrec[i]->key,hw->hrec[j]->key) && !strcmp(hr->hrec[i]->value,hw->hrec[j]->value) ) break;
}
if ( j>=nw_ori )
bcf_hdr_add_hrec(hw, bcf_hrec_dup(hr->hrec[i]));
}
else
{
bcf_hrec_t *rec = bcf_hdr_get_hrec(hw, hr->hrec[i]->type, hr->hrec[i]->vals[0]);
if ( !rec )
bcf_hdr_add_hrec(hw, bcf_hrec_dup(hr->hrec[i]));
}
}
// samples
for (i=0; i<bcf_hdr_nsamples(hr); i++)
{
char *name = hr->samples[i];
if ( bcf_hdr_id2int(hw, BCF_DT_SAMPLE, name)!=-1 )
{
// there is a sample with the same name
int len = strlen(hr->samples[i]) + strlen(clash_prefix) + 1;
name = (char*) malloc(sizeof(char)*(len+1));
sprintf(name,"%s:%s",clash_prefix,hr->samples[i]);
bcf_hdr_add_sample(hw,name);
free(name);
}
else
bcf_hdr_add_sample(hw,name);
}
}
