} else {
b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdin), mode);
}
-#ifndef BCF_LITE
- b->fp->owned_file = 1;
-#endif
return b;
}
ks_tokaux_t aux;
// set ref, alt, flt, info, fmt
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;
+ for (p = b->str, n = 0; p < b->str + b->l_str; ++p) {
+ if (*p == 0 && p+1 != b->str + b->l_str) {
+ if (n == 5) {
+ ++n;
+ break;
+ } else tmp[n++] = p + 1;
+ }
+ }
if (n != 5) {
- fprintf(stderr, "[%s] incorrect number of fields (%d != 5). Corrupted file?\n", __func__, n);
+ fprintf(stderr, "[%s] incorrect number of fields (%d != 5) at %d:%d\n", __func__, n, b->tid, b->pos);
return -1;
}
b->ref = tmp[0]; b->alt = tmp[1]; b->flt = tmp[2]; b->info = tmp[3]; b->fmt = tmp[4];
for (i = 0; i < b->n_gi; ++i) {
if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2;
- } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("HQ", 2)) {
+ } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("HQ", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
b->gi[i].len = 2;
- } else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)
- || b->gi[i].fmt == bcf_str2int("SP", 2))
- {
+ } 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("SP", 2)) {
+ b->gi[i].len = 4;
} else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2 * 4;
}
}
bgzf_read(bp->fp, b->str, b->l_str);
l = 12 + b->l_str;
- bcf_sync(b);
+ if (bcf_sync(b) < 0) return -2;
for (i = 0; i < b->n_gi; ++i) {
bgzf_read(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
l += b->gi[i].len * h->n_smpl;
}
x = b->n_alleles * (b->n_alleles + 1) / 2;
if (b->n_gi == 0) return;
+ int iPL = -1;
+ if ( b->n_alleles > 2 ) {
+ for (i=0; i<b->n_gi; i++) {
+ if ( b->gi[i].fmt == bcf_str2int("PL", 2) ) {
+ iPL = i;
+ break;
+ }
+ }
+ }
for (j = 0; j < h->n_smpl; ++j) {
+
+ // Determine GT with maximum PL (multiple ALT sites only)
+ int imax=-1;
+ if ( iPL!=-1 ) {
+ uint8_t *d = (uint8_t*)b->gi[iPL].data + j * x;
+ int k,identical=1;
+ imax=0;
+ for (k=1; k<x; k++)
+ {
+ if ( identical && d[k]!=d[k-1] ) identical = 0;
+ if ( d[k]<d[imax] ) imax = k;
+ }
+ // If all lks are identical, leave GT untouched
+ if ( identical ) imax = -1;
+ }
kputc('\t', s);
for (i = 0; i < b->n_gi; ++i) {
if (i) kputc(':', s);
if (k > 0) kputc(',', s);
kputw(d[k], s);
}
- } 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)) {
kputw(((uint16_t*)b->gi[i].data)[j], s);
- } 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)) {
kputw(((uint8_t*)b->gi[i].data)[j], s);
+ } else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
+ kputw(((int32_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];
- if (y>>7&1) {
- kputsn("./.", 3, s);
- } else {
- kputc('0' + (y>>3&7), s);
- kputc("/|"[y>>6&1], s);
- kputc('0' + (y&7), s);
- }
+ int y = ((uint8_t*)b->gi[i].data)[j];
+ if ( y>>7&1 )
+ kputsn("./.", 3, s);
+ else if ( imax==-1 )
+ {
+ kputc('0' + (y>>3&7), s);
+ kputc("/|"[y>>6&1], s);
+ kputc('0' + (y&7), s);
+ }
+ else
+ {
+ // Arguably, the while loop will be faster than two sqrts
+ int n = 0;
+ int row = 1;
+ while ( n<imax )
+ {
+ row++;
+ n += row;
+ }
+ row--;
+ kputw(imax-n+row, s);
+ kputc("/|"[y>>6&1], s);
+ kputw(row, s);
+ }
} else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
float *d = (float*)b->gi[i].data + j * x;
int k;
if (k > 0) kputc(',', s);
ksprintf(s, "%.2f", d[k]);
}
- }
+ } else kputc('.', s); // custom fields
}
}
}