/*
f - previous estimate of the 4 possible haplotype frequencies (in normal scale)
s1 - GLs (in log scale) for site1 for all "n" individuals
s2 - GLs (in log scale) for site2 for all "n" individuals
n - number of individuals
*/
int pair_freq_iter_log(double f[4], double **s1, double **s2, uint64_t n)
{
double ff[4];
int k, h;
// Convert haplot frequencies to log-scale
conv_space(f, 4, log);
for (k = 0; k < 4; ++k)
ff[k] = -INFINITY;
for (uint64_t i = 0; i < n; ++i) {
double *p[2], sum, tmp;
p[0] = s1[i];
p[1] = s2[i];
sum = -INFINITY;
for (k = 0; k < 4; ++k)
for (h = 0; h < 4; ++h)
sum = logsum(sum, f[k] + f[h] + p[0][_G1(k,h)] + p[1][_G2(k,h)]);
for (k = 0; k < 4; ++k) {
tmp = -INFINITY;
for (h = 0; h < 4; ++h)
logsum(tmp, f[k] + f[h] + logsum(p[0][_G1(h,k)] + p[1][_G2(h,k)], p[0][_G1(k,h)] + p[1][_G2(k,h)]));
ff[k] = logsum(ff[k], tmp - sum);
}
}
// Calculate frequency
for (k = 0; k < 4; ++k)
f[k] = exp(ff[k]) / (2 * n);
// Normalize
for (k = 0; k < 4; k++)
f[k] /= f[0] + f[1] + f[2] + f[3];
return 0;
}
int pair_freq_iter(double f[4], double **s1, double **s2, uint64_t n)
{
double ff[4];
int k, h;
memset(ff, 0, 4 * sizeof(double));
for (uint64_t i = 0; i < n; ++i) {
double *p[2], sum, tmp;
p[0] = s1[i];
p[1] = s2[i];
sum = 0;
for (k = 0; k < 4; ++k)
for (h = 0; h < 4; ++h)
sum += f[k] * f[h] * p[0][_G1(k,h)] * p[1][_G2(k,h)];
for (k = 0; k < 4; ++k) {
tmp = 0;
for (h = 0; h < 4; ++h)
tmp += f[k] * f[h] * (p[0][_G1(h,k)] * p[1][_G2(h,k)] + p[0][_G1(k,h)] * p[1][_G2(k,h)]);
ff[k] += tmp / sum;
}
}
// Calculate frequency
for (k = 0; k < 4; ++k)
f[k] = ff[k] / (2 * n);
// Normalize
for (k = 0; k < 4; k++)
f[k] /= f[0] + f[1] + f[2] + f[3];
return 0;
}
// 0: the previous site; 1: the current site
static int pair_freq_iter(int n, double *pdg[2], double f[4])
{
double ff[4];
int i, k, h;
// printf("%lf,%lf,%lf,%lf\n", f[0], f[1], f[2], f[3]);
memset(ff, 0, 4 * sizeof(double));
for (i = 0; i < n; ++i) {
double *p[2], sum, tmp;
p[0] = pdg[0] + i * 3; p[1] = pdg[1] + i * 3;
for (k = 0, sum = 0.; k < 4; ++k)
for (h = 0; h < 4; ++h)
sum += f[k] * f[h] * p[0][_G1(k,h)] * p[1][_G2(k,h)];
for (k = 0; k < 4; ++k) {
tmp = f[0] * (p[0][_G1(0,k)] * p[1][_G2(0,k)] + p[0][_G1(k,0)] * p[1][_G2(k,0)])
+ f[1] * (p[0][_G1(1,k)] * p[1][_G2(1,k)] + p[0][_G1(k,1)] * p[1][_G2(k,1)])
+ f[2] * (p[0][_G1(2,k)] * p[1][_G2(2,k)] + p[0][_G1(k,2)] * p[1][_G2(k,2)])
+ f[3] * (p[0][_G1(3,k)] * p[1][_G2(3,k)] + p[0][_G1(k,3)] * p[1][_G2(k,3)]);
ff[k] += f[k] * tmp / sum;
}
}
for (k = 0; k < 4; ++k) f[k] = ff[k] / (2 * n);
return 0;
}
