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#ifndef PHYLO_P_H
#define PHYLO_P_H
#include <stdlib.h>
#include <stdio.h>
#include <getopt.h>
#include <misc.h>
#include <msa.h>
#include <maf.h>
#include <tree_model.h>
#include <sufficient_stats.h>
#include <subst_distrib.h>
#include <prob_vector.h>
#include <prob_matrix.h>
#include "list_of_lists.h"
#include "phylo_p_print.h"
#include "fit_column.h"
#include "fit_feature.h"
/* default values for epsilon; can tolerate larger value with --wig-scores or
--base-by-base */
#define DEFAULT_EPSILON 1e-10
#define DEFAULT_EPSILON_BASE_BY_BASE 1e-6
typedef enum{SPH, LRT, SCORE, GERP} method_type;
/* maximum size of matrix for which to do explicit convolution of
joint prior; beyond this size an approximation is used.
Computational complexity is proportional to square of this number.
This only comes into play when --features and --subtree are used
together */
#define MAX_CONVOLVE_SIZE 22500
struct phyloP_struct {
MSA *msa;
int prior_only, post_only, quantiles_only;
int output_wig, output_gff;
int nsites, fit_model, base_by_base, default_epsilon, refidx, refidx_feat;
double ci, epsilon;
char *subtree_name, *chrom;
List *branch_name;
GFF_Set *feats;
method_type method;
mode_type mode;
FILE *outfile, *logf;
TreeModel *mod;
List *cats_to_do;
CategoryMap *cm;
char *help, *mod_fname, *msa_fname;
ListOfLists *results;
int no_prune;
};
struct phyloP_struct *phyloP_struct_new(int rphast);
void phyloP(struct phyloP_struct *p);
#endif
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