}
}
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;
- }
+ int ploidy = b->ploidy ? b->ploidy[j] : 2;
kputc('\t', s);
for (i = 0; i < b->n_gi; ++i) {
if (i) kputc(':', s);
if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
uint8_t *d = (uint8_t*)b->gi[i].data + j * x;
int k;
- for (k = 0; k < x; ++k) {
- if (k > 0) kputc(',', s);
- kputw(d[k], s);
- }
+ if ( ploidy==1 )
+ for (k=0; k<b->n_alleles; k++)
+ {
+ if (k>0) kputc(',', s);
+ kputw(d[(k+1)*(k+2)/2-1], s);
+ }
+ else
+ for (k = 0; k < x; ++k) {
+ if (k > 0) kputc(',', s);
+ kputw(d[k], s);
+ }
} 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)) {
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 if ( imax==-1 )
+ if ( ploidy==1 )
{
- kputc('0' + (y>>3&7), s);
- kputc("/|"[y>>6&1], s);
- kputc('0' + (y&7), s);
+ if ( y>>7&1 )
+ kputc('.', s);
+ else
+ kputc('0' + (y>>3&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;
+ if ( y>>7&1 )
+ kputsn("./.", 3, s);
+ else {
+ kputc('0' + (y>>3&7), s);
+ kputc("/|"[y>>6&1], s);
+ kputc('0' + (y&7), s);
}
- 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;
return 0;
}
+int remove_tag(char *str, const char *tag, char delim)
+{
+ char *tmp = str, *p;
+ int len_diff = 0, ori_len = strlen(str);
+ while ( *tmp && (p = strstr(tmp,tag)) )
+ {
+ if ( p>str )
+ {
+ if ( *(p-1)!=delim ) { tmp=p+1; continue; } // shared substring
+ p--;
+ }
+ char *q=p+1;
+ while ( *q && *q!=delim ) q++;
+ if ( p==str && *q ) q++; // the tag is first, don't move the delim char
+ len_diff += q-p;
+ if ( ! *q ) { *p = 0; break; } // the tag was last, no delim follows
+ else
+ memmove(p,q,ori_len-(int)(p-str)-(int)(q-p)); // *q==delim
+ }
+ if ( len_diff==ori_len )
+ str[0]='.', str[1]=0, len_diff--;
+
+ return len_diff;
+}
+
+
+void rm_info(kstring_t *s, const char *key)
+{
+ char *p = s->s;
+ int n = 0;
+ while ( n<4 )
+ {
+ if ( !*p ) n++;
+ p++;
+ }
+ char *q = p+1;
+ while ( *q && q-s->s<s->l ) q++;
+
+ int nrm = remove_tag(p, key, ';');
+ if ( nrm )
+ memmove(q-nrm, q, s->s+s->l-q+1);
+ s->l -= nrm;
+}
+
int bcf_cpy(bcf1_t *r, const bcf1_t *b)
{
char *t1 = r->str;