/*
Genome-wide Efficient Mixed Model Association (GEMMA)
Copyright © 2011-2017, Xiang Zhou
Copyright © 2017, Peter Carbonetto
Copyright © 2017, Pjotr Prins
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 "gsl/gsl_matrix.h"
#include "gsl/gsl_vector.h"
#include <algorithm>
#include <map>
#include <vector>
#include <cstdint>
#include "gzstream.h"
#include "param.h"
#define tab(col) ( col ? "\t" : "")
constexpr uint8_t CHR_X = 'X';
constexpr uint8_t CHR_Y = 'Y';
constexpr uint8_t CHR_M = 'M';
using namespace std;
void ProgressBar(string str, double p, double total, double ratio = -1.0);
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_bimbam_geno(const string &file_geno, const set<string> &setSnps,
const gsl_matrix *W, const 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);
gsl_matrix *mdb_calc_kin(const string file_geno, const int k_mode, const string loco);
bool BimbamKin(const string file_geno, const set<string> ksnps,
vector<int> &indicator_snp, const int k_mode,
const int display_pace, gsl_matrix *matrix_kin,
const bool test_nind);
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_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 BimbamKinUncentered(const string &file_geno, const set<string> ksnps,
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 set<string> setKSnps, 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);
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
