https://github.com/ekg/freebayes
Tip revision: 60850dc518fc453622cbb40ad6dd9f67644ed859 authored by Pjotr Prins on 16 December 2020, 10:18:06 UTC
Disable cmake, but leave the file with a message
Disable cmake, but leave the file with a message
Tip revision: 60850dc
DataLikelihood.h
#ifndef __DATALIKELIHOOD_H
#define __DATALIKELIHOOD_H
#include <iostream>
#include <vector>
#include <utility> // pair
#include <algorithm>
#include <numeric>
#include <vector>
#include <iterator>
#include <cmath>
#include "Allele.h"
#include "Sample.h"
#include "Genotype.h"
#include "Utility.h"
#include "Multinomial.h"
#include "Dirichlet.h"
#include "Bias.h"
#include "Contamination.h"
#include "AlleleParser.h"
#include "ResultData.h"
using namespace std;
long double
probObservedAllelesGivenGenotype(
Sample& sample,
Genotype& genotype,
Bias& observationBias,
vector<Allele>& genotypeAlleles,
Contamination& contaminations,
map<string, double>& freqs,
Parameters& parameters);
vector<pair<Genotype*, long double> >
probObservedAllelesGivenGenotypes(
Sample& sample,
vector<Genotype*>& genotypes,
Bias& observationBias,
vector<Allele>& genotypeAlleles,
Contamination& contaminations,
map<string, double>& freqs,
Parameters& parameters);
void
calculateSampleDataLikelihoods(
Samples& samples,
Results& results,
AlleleParser* parser,
map<int, vector<Genotype> >& genotypesByPloidy,
Parameters& parameters,
bool usingNull,
Bias& observationBias,
vector<Allele>& genotypeAlleles,
Contamination& contaminationEstimates,
map<string, double>& estimatedAlleleFrequencies,
map<string, vector<vector<SampleDataLikelihood> > >& sampleDataLikelihoodsByPopulation,
map<string, vector<vector<SampleDataLikelihood> > >& variantSampleDataLikelihoodsByPopulation,
map<string, vector<vector<SampleDataLikelihood> > >& invariantSampleDataLikelihoodsByPopulation);
#endif