+ int dret, k, i, sync = 0;
+ vcf_t *v = (vcf_t*)bp->v;
+ char *p, *q;
+ kstring_t str, rn;
+ ks_tokaux_t aux, a2;
+ if (!bp->is_vcf) return bcf_read(bp, h, b);
+ v->line.l = 0;
+ 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
+ int tid = bcf_str2id(v->refhash, p);
+ if (tid < 0) {
+ tid = bcf_str2id_add(v->refhash, strdup(p));
+ kputs(p, &rn); kputc('\0', &rn);
+ sync = 1;
+ }
+ b->tid = tid;
+ } else if (k == 1) { // pos
+ b->pos = atoi(p) - 1;
+ } else if (k == 5) { // qual
+ b->qual = (p[0] >= '0' && p[0] <= '9')? atof(p) : 0;
+ } 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(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)) {
+ ((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) || 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;
+ memset((uint8_t*)b->gi[i].data + (k - 9) * y, 0, y);
+ } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
+ int y = b->n_alleles * (b->n_alleles + 1) / 2;
+ memset((float*)b->gi[i].data + (k - 9) * y, 0, y * 4);
+ }
+ }
+ goto endblock;
+ }
+ 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)) {
+ 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) || 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;
+ } else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
+ int x, y, j;
+ uint8_t *data = (uint8_t*)b->gi[i].data;
+ y = b->n_alleles * (b->n_alleles + 1) / 2;
+ for (j = 0; j < y; ++j) {
+ x = strtol(q, &q, 10);
+ if (x > 255) x = 255;
+ data[(k-9) * y + j] = x;
+ ++q;
+ }
+ } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
+ int j, y;
+ float x, *data = (float*)b->gi[i].data;
+ y = b->n_alleles * (b->n_alleles + 1) / 2;
+ for (j = 0; j < y; ++j) {
+ x = strtod(q, &q);
+ data[(k-9) * y + j] = x > 0? -x/10. : x;
+ ++q;
+ }
+ }
+ }
+ endblock: i = i;
+ }
+ }
+ h->l_nm = rn.l; h->name = rn.s;
+ if (sync) bcf_hdr_sync(h);
+ return v->line.l + 1;