memset(&smpl, 0, sizeof(kstring_t));
while (ks_getuntil(v->ks, '\n', &v->line, &dret) >= 0) {
if (v->line.l < 2) continue;
- if (v->line.s[0] != '#') return 0; // no sample line
+ if (v->line.s[0] != '#') {
+ free(meta.s);
+ free(smpl.s);
+ free(h);
+ return 0; // no sample line
+ }
if (v->line.s[0] == '#' && v->line.s[1] == '#') {
kputsn(v->line.s, v->line.l, &meta); kputc('\n', &meta);
} else if (v->line.s[0] == '#') {
if (!bp->is_vcf) return bcf_hdr_write(bp, h);
if (h->l_txt > 0) {
if (strstr(h->txt, "##fileformat=")) has_ver = 1;
- if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.0\n");
+ if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n");
fwrite(h->txt, 1, h->l_txt - 1, v->fpout);
}
- if (h->l_txt == 0) fprintf(v->fpout, "##fileformat=VCFv4.0\n");
+ if (h->l_txt == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n");
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]);
((uint8_t*)b->gi[i].data)[k-9] = 0;
} else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
((int32_t*)b->gi[i].data)[k-9] = 0;
- } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
+ } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
((uint16_t*)b->gi[i].data)[k-9] = 0;
} else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
int y = b->n_alleles * (b->n_alleles + 1) / 2;
int x = strtol(q, &q, 10);
if (x > 0xffff) x = 0xffff;
((uint32_t*)b->gi[i].data)[k-9] = x;
- } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
+ } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
int x = strtol(q, &q, 10);
if (x > 0xffff) x = 0xffff;
((uint16_t*)b->gi[i].data)[k-9] = x;