https://github.com/ekg/freebayes
Tip revision: 9755e43db74f9fa8ad2653d6a771d7a8d148ee66 authored by Erik Garrison on 10 December 2013, 00:24:08 UTC
Setting Release-Version v0.9.10
Setting Release-Version v0.9.10
Tip revision: 9755e43
Dirichlet.cpp
#include "Dirichlet.h"
#include "Sum.h"
#include "Product.h"
#include <iostream>
long double dirichlet(const vector<long double>& probs,
const vector<int>& obs,
long double s) {
vector<long double> alphas;
for (vector<int>::const_iterator o = obs.begin(); o != obs.end(); ++o)
alphas.push_back(*o + 1 * s);
vector<long double> obsProbs;
vector<long double>::const_iterator a = alphas.begin();
vector<long double>::const_iterator p = probs.begin();
for (; p != probs.end() && a != alphas.end(); ++p, ++a) {
obsProbs.push_back(pow(*p, *a - 1));
}
return 1.0 / beta(alphas) * product(obsProbs);
}
long double dirichletMaximumLikelihoodRatio(const vector<long double>& probs,
const vector<int>& obs,
long double s) {
long double maximizingObs = obs.size() / sum(obs);
vector<int> m(obs.size(), maximizingObs);
return dirichlet(probs, obs, s) / dirichlet(probs, m, s);
}
// XXX the logspace versions are broken
long double dirichletln(const vector<long double>& probs,
const vector<int>& obs,
long double s) {
vector<long double> alphas;
for (vector<int>::const_iterator o = obs.begin(); o != obs.end(); ++o)
alphas.push_back(*o + 1 * s);
vector<long double> obsProbs;
vector<long double>::const_iterator a = alphas.begin();
vector<long double>::const_iterator p = probs.begin();
for (; p != probs.end() && a != alphas.end(); ++p, ++a) {
obsProbs.push_back(powln(log(*p), *a - 1));
}
return log(1.0) - (betaln(alphas) + sum(obsProbs));
}
long double dirichletMaximumLikelihoodRatioln(const vector<long double>& probs,
const vector<int>& obs,
long double s) {
long double maximizingObs = (long double) obs.size() / (long double) sum(obs);
vector<int> m(obs.size(), maximizingObs);
return dirichletln(probs, obs, s) - dirichletln(probs, m, s);
}