ngsF-HMM.hpp

#pragma once

#include "read_data.hpp"
#include "HMM.hpp"
#include "threadpool.h"
#include "bfgs.h"

extern bool SIG_COND;
const uint64_t N_STATES = 2;
extern char const* version;

// Struct to store all input arguments
typedef struct {
  char *in_geno;
  char *in_pos;
  bool in_bin;
  bool in_lkl;
  bool in_loglkl;
  uint64_t n_ind;
  uint64_t n_sites;
  bool call_geno;
  char *in_freq;
  int freq_est;
  int e_prob_calc;
  char *in_indF;
  bool indF_fixed;
  bool alpha_fixed;
  char *out_prefix;
  unsigned int log;
  bool log_bin;
  uint min_iters;
  uint max_iters;
  double min_epsilon;
  uint n_threads;
  uint verbose;
  uint seed;

  double ***geno_lkl;    // n_ind * n_sites+1 * N_GENO
  double ***geno_lkl_s;  // n_sites+1 * n_ind * N_GENO
  double *pos_dist;      // n_sites+1
  double *freq;          // n_sites+1
  double ***e_prob;      // n_ind * n_sites+1 * N_STATES
  char **path;           // n_ind * n_sites+1
  double ***marg_prob;   // n_ind * n_sites+1 * N_STATES
  double *indF;          // n_ind
  double *alpha;         // n_ind
  double *ind_lkl;       // n_ind
  double prev_tot_lkl;
  double tot_lkl;

  threadpool_t *thread_pool;
} params;


// parse_args.cpp
void init_pars(params* );
void parse_cmd_args(params*, int, char**);
int init_output(params*);

// EM.cpp
int EM(params*);
void iter_EM(params*);
void print_iter(char*, params*);
void dump_data(gzFile, params*, bool = false);