static double mc_cal_afs(bcf_p1aux_t *ma, double *p_ref_folded, double *p_var_folded)
{
int k;
long double sum = 0., sum2;
double *phi = ma->is_indel? ma->phi_indel : ma->phi;
memset(ma->afs1, 0, sizeof(double) * (ma->M + 1));
mc_cal_y(ma);
// compute AFS
for (k = 0, sum = 0.; k <= ma->M; ++k)
sum += (long double)phi[k] * ma->z[k];
for (k = 0; k <= ma->M; ++k) {
ma->afs1[k] = phi[k] * ma->z[k] / sum;
if (isnan(ma->afs1[k]) || isinf(ma->afs1[k])) return -1.;
}
// compute folded variant probability
for (k = 0, sum = 0.; k <= ma->M; ++k)
sum += (long double)(phi[k] + phi[ma->M - k]) / 2. * ma->z[k];
for (k = 1, sum2 = 0.; k < ma->M; ++k)
sum2 += (long double)(phi[k] + phi[ma->M - k]) / 2. * ma->z[k];
*p_var_folded = sum2 / sum;
*p_ref_folded = (phi[k] + phi[ma->M - k]) / 2. * (ma->z[ma->M] + ma->z[0]) / sum;
// the expected frequency
for (k = 0, sum = 0.; k <= ma->M; ++k) {
ma->afs[k] += ma->afs1[k];
sum += k * ma->afs1[k];
}
return sum / ma->M;
}
static double mc_cal_afs(bcf_p1aux_t *ma)
{
int k;
long double sum = 0.;
memset(ma->afs1, 0, sizeof(double) * (ma->M + 1));
mc_cal_y(ma);
for (k = 0, sum = 0.; k <= ma->M; ++k)
sum += (long double)ma->phi[k] * ma->z[k];
for (k = 0; k <= ma->M; ++k) {
ma->afs1[k] = ma->phi[k] * ma->z[k] / sum;
if (isnan(ma->afs1[k]) || isinf(ma->afs1[k])) return -1.;
}
for (k = 0, sum = 0.; k <= ma->M; ++k) {
ma->afs[k] += ma->afs1[k];
sum += k * ma->afs1[k];
}
return sum / ma->M;
}
