void pp_save_r(int n, int prime, int power) {
pp_pp* pp = &pppp[power];
pp_value* v;
int i, raise;
mpq_t q;
if (!pp->p)
new_pp(pp, prime, power);
QINIT(&q, "pp_save_r temp");
mpq_set_ui(q, 1, n);
pp_save_any(pp, q, n, 1);
QCLEAR(&q, "pp_save_r temp");
}
void HaploWindow::prunePhase(int i, double t)
{
// pp[i][z]
// hap1[i][z]
// hap2[i][z]
// skip[z]
if ( (!haplo->include[i]) ||(!ambig[i]))
return;
MultiLocusGenotype * mlg = genoGroup[i];
double psum = 0;
vector<double> new_pp(0);
vector<int> new_h1(0);
vector<int> new_h2(0);
vector<bool> new_skip(0);
for (int z=0; z < hap1[i].size(); z++)
{
if ( pp[i][z] >= t )
{
new_pp.push_back(pp[i][z]);
psum += pp[i][z];
new_h1.push_back(hap1[i][z]);
new_h2.push_back(hap2[i][z]);
new_skip.push_back(mlg->skip[z]);
}
}
// Normalise?
if (pp[i].size() > new_pp.size() )
{
for (int z=0; z < new_pp.size(); z++)
new_pp[z] /= psum;
}
// Update
pp[i] = new_pp;
hap1[i] = new_h1;
hap2[i] = new_h2;
mlg->skip = new_skip;
}