estimator.h

/* The MIT License

   Copyright (c) 2014 Adrian Tan <atks@umich.edu>

   Permission is hereby granted, free of charge, to any person obtaining a copy
   of this software and associated documentation files (the "Software"), to deal
   in the Software without restriction, including without limitation the rights
   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
   copies of the Software, and to permit persons to whom the Software is
   furnished to do so, subject to the following conditions:

   The above copyright notice and this permission notice shall be included in
   all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
   THE SOFTWARE.
*/

#ifndef ESTIMATORS_H
#define ESTIMATORS_H

#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <ctype.h>
#include <math.h>
#include <string>
#include <iostream>
#include <fstream>
#include <algorithm>
#include <vector>
#include <map>
#include <limits.h>
#include <float.h>
#include "utils.h"
#include "hts_utils.h"
#include "log_tool.h"
#include "Rmath/Rmath.h"

/**
 * Class containing estimating methods of common features.
 */
class Estimator
{
    public:
    //log tool for log space computations.
    LogTool *lt;

    /**
     * Constructor.
     */
    Estimator()
    {
        lt = new LogTool();
    };

    /**
     * Constructor.
     */
    Estimator(LogTool *lt)
    {
        this->lt = lt;
    };
    
    /**
     * Computes allele frequencies using hard calls.
     *
     * @gts        - genotypes
     * @no_samples - number of samples
     * @ploidy     - ploidy
     * @no_alleles - number of alleles
     * @AC         - alternate allele counts
     * @AN         - total number of allele counts
     * @AF         - alternate allele frequency
     * @GC         - genotype counts
     * @GN         - total number of genotype counts
     * @GF         - genotype frequency
     * @NS         - number of samples with data
     */
    void compute_af(int32_t *gts, int32_t no_samples, int32_t ploidy,
                    int32_t no_alleles, int32_t *AC, int32_t& AN, float *AF, 
                    int32_t *GC,  int32_t& GN, float *GF, int32_t& NS);
                
    /**
     * Computes allele frequencies using EM algorithm from genotype likelihoods
     * under assumption of Hardy-Weinberg Equilibrium.
     *
     * @pls        - PHRED genotype likelihoods
     * @no_samples - number of samples
     * @ploidy     - ploidy
     * @no_alleles - number of alleles
     * @MLE_HWE_AF - estimated AF
     * @MLE_HWE_GF - estimated GF
     * @n          - effective sample size
     * @e          - error
     */
    void compute_gl_af_hwe(int32_t *pls, int32_t no_samples, int32_t ploidy,
                    int32_t no_alleles, float *MLE_HWE_AF, float *MLE_HWE_GF, int32_t& n,
                    double e);

    /**
     * Computes allele frequencies using EM algorithm from genotype likelihoods.
     *
     * @pls        - PHRED genotype likelihoods
     * @nsamples   - number of samples
     * @ploidy     - ploidy
     * @n_alleles  - number of alleles
     * @MLE_AF     - estimated AF
     * @MLE_GF     - estimated GF
     * @n          - effective sample size
     * @e          - error
     */
    void compute_gl_af(int32_t *pls, int32_t nsamples, int32_t ploidy,
                    int32_t n_allele, float *MLE_AF, float *MLE_GF, int32_t& n,
                    double e);

    /**
     * Computes the Hardy-Weinberg Likelihood Ratio Test Statistic
     *
     * @pls        - PHRED genotype likelihoods
     * @no_samples - number of samples
     * @ploidy     - ploidy
     * @no_alleles - number of alleles
     * @MLE_HWE_AF - estimated AF assuming HWE
     * @MLE_GF     - estimated GF
     * @n          - effective sample size
     * @lr         - log10 likelihood ratio
     * @logp       - likelihood ratio test log p-value
     * @df         - degrees of freedom
     *
     */
    void compute_hwe_lrt(int32_t *pls, int32_t no_samples, int32_t ploidy,
                int32_t no_alleles, float *MLE_HWE_GF, float *MLE_GF, int32_t& n,
                float& lr, float& logp, int32_t& df);

    /**
     * Computes the Inbreeding Coefficient Statistic from Genotype likelihoods.
     *
     * @pls        - PHRED genotype likelihoods
     * @no_samples - number of samples
     * @ploidy     - ploidy
     * @GF         - GF
     * @HWE_AF     - AF under HWE assumption
     * @no_alleles - number of alleles
     * @F          - estimated inbreeding coefficient
     * @n          - effective sample size
     */
    void compute_gl_fic(int32_t * pls, int32_t no_samples, int32_t ploidy,
                                   float* HWE_AF, int32_t no_alleles, float* GF,
                                   float& F, int32_t& n);

    /**
     * Computes Allele Balance from genotype likelihoods.
     *
     * @pls        - PHRED genotype likelihoods
     * @no_samples - number of samples
     * @ploidy     - ploidy
     * @dps        - depths
     * @GF         - estimated GF
     * @no_alleles - number of alleles
     * @ab         - estimate of allele balance
     * @n          - effective sample size
     */
    void compute_gl_ab(int32_t *pls, int32_t no_samples, int32_t ploidy,
                    int32_t *dps,
                    float* GF, int32_t no_alleles,
                    float& ab, int32_t& n);


    /**
     * Computes the phred scaled QUAL for a variant.
     *
     * @pls        - PHRED genotype likelihoods
     * @no_samples - number of samples
     * @ploidy     - ploidy
     * @no_alleles - number of alleles
     * @n          - effective sample size
     * @qual       - PHRED scaled QUAL
     */
    void compute_qual(int32_t *pls, int32_t no_samples, int32_t ploidy,
                int32_t no_alleles, float &qual, int32_t &n);

    private:
};

#endif