b->ref = b->alt = b->flt = b->info = b->fmt = 0;
for (p = b->str, n = 0; p < b->str + b->l_str; ++p)
if (*p == 0 && p+1 != b->str + b->l_str) tmp[n++] = p + 1;
- if (n != 5) return -1;
+ if (n != 5) {
+ fprintf(stderr, "[bcf_sync] incorrect number of fields (%d != 5)\n", n);
+ return -1;
+ }
b->ref = tmp[0]; b->alt = tmp[1]; b->flt = tmp[2]; b->info = tmp[3]; b->fmt = tmp[4];
// set n_alleles
- for (p = b->alt, n = 1; *p; ++p)
- if (*p == ',') ++n;
- b->n_alleles = n + 1;
+ if (*b->alt == 0) b->n_alleles = 1;
+ else {
+ for (p = b->alt, n = 1; *p; ++p)
+ if (*p == ',') ++n;
+ b->n_alleles = n + 1;
+ }
// set n_gi and gi[i].fmt
for (p = b->fmt, n = 1; *p; ++p)
if (*p == ':') ++n;
} else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)) {
b->gi[i].len = 1;
} else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
- b->gi[i].len = 4;
+ b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2 * 4;
}
b->gi[i].data = realloc(b->gi[i].data, n_smpl * b->gi[i].len);
}
kputw(((uint8_t*)b->gi[i].data)[j], s);
} else if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
int y = ((uint8_t*)b->gi[i].data)[j];
- kputc('0' + (y>>3&7), s);
- kputc("/|"[y>>6&1], s);
- kputc('0' + (y&7), s);
+ if (y>>7&1) {
+ kputsn("./.", 3, s);
+ } else {
+ kputc('0' + (y>>3&7), s);
+ kputc("/|"[y>>6&1], s);
+ kputc('0' + (y&7), s);
+ }
+ } else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
+ float *d = (float*)b->gi[i].data + j * x;
+ int k;
+ //printf("- %lx\n", d);
+ for (k = 0; k < x; ++k) {
+ if (k > 0) kputc(',', s);
+ ksprintf(s, "%.2f", d[k]);
+ }
}
}
}