static int cal_pdg(const bcf1_t *b, bcf_p1aux_t *ma)
{
- int i, j, k;
+ int i, j;
long *p, tmp;
p = alloca(b->n_alleles * sizeof(long));
memset(p, 0, sizeof(long) * b->n_alleles);
for (j = 0; j < ma->n; ++j) {
const uint8_t *pi = ma->PL + j * ma->PL_len;
double *pdg = ma->pdg + j * 3;
- pdg[0] = ma->q2p[pi[b->n_alleles]]; pdg[1] = ma->q2p[pi[1]]; pdg[2] = ma->q2p[pi[0]];
- for (i = k = 0; i < b->n_alleles; ++i) {
- p[i] += (int)pi[k];
- k += b->n_alleles - i;
- }
+ pdg[0] = ma->q2p[pi[2]]; pdg[1] = ma->q2p[pi[1]]; pdg[2] = ma->q2p[pi[0]];
+ for (i = 0; i < b->n_alleles; ++i)
+ p[i] += (int)pi[(i+1)*(i+2)/2-1];
}
for (i = 0; i < b->n_alleles; ++i) p[i] = p[i]<<4 | i;
for (i = 1; i < b->n_alleles; ++i) // insertion sort