/*
    Genome-wide Efficient Mixed Model Association (GEMMA)
    Copyright (C) 2011-2017, Xiang Zhou

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program. If not, see <http://www.gnu.org/licenses/>.
*/

#ifndef __IO_H__
#define __IO_H__

#include <vector>
#include <map>
#include <algorithm>
#include "gsl/gsl_vector.h"
#include "gsl/gsl_matrix.h"

#include "gzstream.h"
#include "param.h"

using namespace std;

void ProgressBar (string str, double p, double total);
void ProgressBar (string str, double p, double total, double ratio);
std::istream& safeGetline(std::istream& is, std::string& t);

bool ReadFile_snps (const string &file_snps, set<string> &setSnps);
bool ReadFile_snps_header (const string &file_snps, set<string> &setSnps);
bool ReadFile_log (const string &file_log, double &pheno_mean);

bool ReadFile_bim (const string &file_bim, vector<SNPINFO> &snpInfo);
bool ReadFile_fam (const string &file_fam,
		   vector<vector<int> > &indicator_pheno,
		   vector<vector<double> > &pheno,
		   map<string, int> &mapID2num,
		   const vector<size_t> &p_column);

bool ReadFile_cvt (const string &file_cvt,
		   vector<int> &indicator_cvt,
		   vector<vector<double> > &cvt,
		   size_t &n_cvt);
bool ReadFile_anno (const string &file_bim, map<string, string> &mapRS2chr,
		    map<string, long int> &mapRS2bp,
		    map<string, double> &mapRS2cM);
bool ReadFile_pheno (const string &file_pheno,
		     vector<vector<int> > &indicator_pheno,
		     vector<vector<double> > &pheno,
		     const vector<size_t> &p_column);
bool ReadFile_column (const string &file_pheno, vector<int> &indicator_idv,
		      vector<double> &pheno, const int &p_column);

bool ReadFile_geno (const string &file_geno, const set<string> &setSnps,
		    const gsl_matrix *W, vector<int> &indicator_idv,
		    vector<int> &indicator_snp, const double &maf_level,
		    const double &miss_level, const double &hwe_level,
		    const double &r2_level, map<string, string> &mapRS2chr,
		    map<string, long int> &mapRS2bp,
		    map<string, double> &mapRS2cM, vector<SNPINFO> &snpInfo,
		    size_t &ns_test);
bool ReadFile_bed (const string &file_bed, const set<string> &setSnps,
		   const gsl_matrix *W, vector<int> &indicator_idv,
		   vector<int> &indicator_snp, vector<SNPINFO> &snpInfo,
		   const double &maf_level, const double &miss_level,
		   const double &hwe_level, const double &r2_level,
		   size_t &ns_test);
bool Bimbam_ReadOneSNP (const size_t inc, const vector<int> &indicator_idv,
			igzstream &infile, gsl_vector *geno,
			double &geno_mean);
void Plink_ReadOneSNP (const int pos, const vector<int> &indicator_idv,
		       ifstream &infile, gsl_vector *geno, double &geno_mean);

void ReadFile_kin (const string &file_kin, vector<int> &indicator_idv,
		   map<string, int> &mapID2num, const size_t k_mode,
		   bool &error, gsl_matrix *G);
void ReadFile_mk (const string &file_mk, vector<int> &indicator_idv,
		  map<string, int> &mapID2num, const size_t k_mode,
		  bool &error, gsl_matrix *G);
void ReadFile_eigenU (const string &file_u, bool &error, gsl_matrix *U);
void ReadFile_eigenD (const string &file_d, bool &error, gsl_vector *eval);

bool BimbamKin (const string &file_geno, vector<int> &indicator_snp,
		const int k_mode, const int display_pace,
		gsl_matrix *matrix_kin);
bool PlinkKin (const string &file_bed, vector<int> &indicator_snp,
	       const int k_mode, const int display_pace,
	       gsl_matrix *matrix_kin);

bool ReadFile_geno (const string &file_geno, vector<int> &indicator_idv,
		    vector<int> &indicator_snp, gsl_matrix *UtX,
		    gsl_matrix *K, const bool calc_K);
bool ReadFile_bed (const string &file_bed, vector<int> &indicator_idv,
		   vector<int> &indicator_snp, gsl_matrix *UtX,
		   gsl_matrix *K, const bool calc_K);
bool ReadFile_geno (const string &file_geno, vector<int> &indicator_idv,
		    vector<int> &indicator_snp,
		    vector<vector<unsigned char> > &Xt, gsl_matrix *K,
		    const bool calc_K, const size_t ni_test,
		    const size_t ns_test);
bool ReadFile_bed (const string &file_bed, vector<int> &indicator_idv,
		   vector<int> &indicator_snp,
		   vector<vector<unsigned char> > &Xt, gsl_matrix *K,
		   const bool calc_K, const size_t ni_test,
		   const size_t ns_test);

bool ReadFile_est (const string &file_est, const vector<size_t> &est_column,
		   map<string, double> &mapRS2est);

bool CountFileLines (const string &file_input, size_t &n_lines);

bool ReadFile_gene (const string &file_gene, vector<double> &vec_read,
		    vector<SNPINFO> &snpInfo, size_t &ng_total);

bool ReadHeader_io (const string &line, HEADER &header);
bool ReadFile_cat (const string &file_cat, map<string, size_t> &mapRS2cat,
		   size_t &n_vc);
bool ReadFile_mcat (const string &file_mcat, map<string, size_t> &mapRS2cat,
		    size_t &n_vc);

bool ReadFile_catc (const string &file_cat,
		    map<string, vector<double> > &mapRS2catc,
		    size_t &n_cat);
bool ReadFile_mcatc (const string &file_mcat, map<string,
		     vector<double> > &mapRS2catc, size_t &n_cat);

bool BimbamKin (const string &file_geno, const int display_pace,
		const vector<int> &indicator_idv,
		const vector<int> &indicator_snp,
		const map<string, double> &mapRS2weight,
		const map<string, size_t> &mapRS2cat,
		const vector<SNPINFO> &snpInfo, const gsl_matrix *W,
		gsl_matrix *matrix_kin, gsl_vector *vector_ns);
bool PlinkKin (const string &file_bed, const int display_pace,
	       const vector<int> &indicator_idv,
	       const vector<int> &indicator_snp,
	       const map<string, double> &mapRS2weight,
	       const map<string, size_t> &mapRS2cat,
	       const vector<SNPINFO> &snpInfo,
	       const gsl_matrix *W, gsl_matrix *matrix_kin,
	       gsl_vector *vector_ns);
bool MFILEKin (const size_t mfile_mode, const string &file_mfile,
	       const int display_pace, const vector<int> &indicator_idv,
	       const vector<vector<int> > &mindicator_snp,
	       const map<string, double> &mapRS2weight,
	       const map<string, size_t> &mapRS2cat,
	       const vector<vector<SNPINFO> > &msnpInfo,
	       const gsl_matrix *W, gsl_matrix *matrix_kin,
	       gsl_vector *vector_ns);

bool ReadFile_wsnp (const string &file_wsnp,
		    map<string, double> &mapRS2double);
bool ReadFile_wsnp (const string &file_wcat, const size_t n_vc,
		    map<string, vector<double> > &mapRS2vector);

void ReadFile_beta (const string &file_beta,
		    const map<string, size_t> &mapRS2cat,
		    const map<string, double> &mapRS2wA,
		    vector<size_t> &vec_cat, vector<size_t> &vec_ni,
		    vector<double> &vec_weight, vector<double> &vec_z2,
		    size_t &ni_total, size_t &ns_total, size_t &ns_test);
void ReadFile_beta (const string &file_beta,
		    const map<string, double> &mapRS2wA,
		    map<string, string> &mapRS2A1,
		    map<string, double> &mapRS2z);
void Calcq (const size_t n_block, const vector<size_t> &vec_cat,
	    const vector<size_t> &vec_ni,
	    const vector<double> &vec_weight, const vector<double> &vec_z2,
	    gsl_matrix *Vq, gsl_vector *q, gsl_vector *s);

void ReadFile_study (const string &file_study, gsl_matrix *Vq,
		     gsl_vector *q_vec, gsl_vector *s_vec, size_t &ni);
void ReadFile_ref (const string &file_ref, gsl_matrix *S_mat,
		   gsl_matrix *Svar_mat, gsl_vector *s_vec, size_t &ni);
void ReadFile_mstudy (const string &file_mstudy, gsl_matrix *Vq,
		      gsl_vector *q_vec, gsl_vector *s_vec, size_t &ni);
void ReadFile_mref (const string &file_mref, gsl_matrix *S_mat,
		    gsl_matrix *Svar_mat, gsl_vector *s_vec, size_t &ni);

// WJA added.
bool bgenKin (const string &file_geno, vector<int> &indicator_snp,
	      const int k_mode, const int display_pace,
	      gsl_matrix *matrix_kin);
bool ReadFile_bgen(const string &file_bgen, const set<string> &setSnps,
		   const gsl_matrix *W, vector<int> &indicator_idv,
		   vector<int> &indicator_snp, vector<SNPINFO> &snpInfo,
		   const double &maf_level, const double &miss_level,
		   const double &hwe_level, const double &r2_level,
		   size_t &ns_test);
bool ReadFile_sample(const string &file_sample,
		     vector<vector<int> > &indicator_pheno,
		     vector<vector<double> > &pheno,
		     const vector<size_t> &p_column,
		     vector<int> &indicator_cvt,
		     vector<vector<double> > &cvt,
		     size_t &n_cvt);

#endif