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]);
str.l = 0; str.m = b->m_str; str.s = b->str;
rn.l = rn.m = h->l_nm; rn.s = h->name;
if (ks_getuntil(v->ks, '\n', &v->line, &dret) < 0) return -1;
+ b->n_smpl = h->n_smpl;
for (p = kstrtok(v->line.s, "\t", &aux), k = 0; p; p = kstrtok(0, 0, &aux), ++k) {
*(char*)aux.p = 0;
if (k == 0) { // ref
} else if (k <= 8) { // variable length strings
kputs(p, &str); kputc('\0', &str);
b->l_str = str.l; b->m_str = str.m; b->str = str.s;
- if (k == 8) bcf_sync(h->n_smpl, b);
+ if (k == 8) bcf_sync(b);
} else { // k > 9
if (strncmp(p, "./.", 3) == 0) {
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)) {
+ } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
((uint8_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;
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)) {
+ } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("SP", 2)) {
double _x = strtod(q, &q);
int x = (int)(_x + .499);
if (x > 255) x = 255;