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]);
for (i = 0; i < b->n_gi; ++i) {
if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
((uint8_t*)b->gi[i].data)[k-9] = 1<<7;
- } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
+ } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
((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)) {
((uint16_t*)b->gi[i].data)[k-9] = 0;
} else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
for (q = kstrtok(p, ":", &a2), i = 0; q && i < b->n_gi; q = kstrtok(0, 0, &a2), ++i) {
if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
((uint8_t*)b->gi[i].data)[k-9] = (q[0] - '0')<<3 | (q[2] - '0') | (q[1] == '/'? 0 : 1) << 6;
- } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
+ } else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
double _x = strtod(q, &q);
int x = (int)(_x + .499);
if (x > 255) x = 255;
((uint8_t*)b->gi[i].data)[k-9] = x;
+ } else if (b->gi[i].fmt == bcf_str2int("SP", 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)) {
int x = strtol(q, &q, 10);
if (x > 0xffff) x = 0xffff;