int vcf_hdr_write(bcf_t *bp, const bcf_hdr_t *h)
{
vcf_t *v = (vcf_t*)bp->v;
- int i;
+ int i, has_ref = 0, has_ver = 0;
if (!bp->is_vcf) return bcf_hdr_write(bp, h);
- if (h->l_txt > 0) fwrite(h->txt, 1, h->l_txt - 1, v->fpout);
+ if (h->l_txt > 0) {
+ if (strstr(h->txt, "##fileformat=")) has_ver = 1;
+ if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.0\n");
+ fwrite(h->txt, 1, h->l_txt - 1, v->fpout);
+ if (strstr(h->txt, "##SQ=")) has_ref = 1;
+ }
+ if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.0\n");
+ if (!has_ref) {
+ fprintf(v->fpout, "##SQ=");
+ for (i = 0; i < h->n_ref; ++i) {
+ fprintf(v->fpout, "%s", h->ns[i]);
+ fputc(i == h->n_ref - 1? '\n' : ',', v->fpout);
+ }
+ }
fprintf(v->fpout, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
for (i = 0; i < h->n_smpl; ++i)
fprintf(v->fpout, "\t%s", h->sns[i]);