From 421355faac3b1aae1fb165fd99ff8f393d3c492a Mon Sep 17 00:00:00 2001 From: DannyArends Date: Wed, 28 Feb 2018 16:22:03 +0100 Subject: io.h is a std lib function for MinGW64, renamed it to gemma_io.h --- src/gemma_io.h | 187 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 187 insertions(+) create mode 100644 src/gemma_io.h (limited to 'src/gemma_io.h') diff --git a/src/gemma_io.h b/src/gemma_io.h new file mode 100644 index 0000000..dd1d5c0 --- /dev/null +++ b/src/gemma_io.h @@ -0,0 +1,187 @@ +/* + 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 . +*/ + +#ifndef __IO_H__ +#define __IO_H__ + +#include "gsl/gsl_matrix.h" +#include "gsl/gsl_vector.h" +#include +#include +#include + +#include "gzstream.h" +#include "param.h" + +#define tab(col) ( col ? "\t" : "") + +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 &setSnps); +bool ReadFile_snps_header(const string &file_snps, set &setSnps); +bool ReadFile_log(const string &file_log, double &pheno_mean); + +bool ReadFile_bim(const string &file_bim, vector &snpInfo); +bool ReadFile_fam(const string &file_fam, vector> &indicator_pheno, + vector> &pheno, map &mapID2num, + const vector &p_column); + +bool ReadFile_cvt(const string &file_cvt, vector &indicator_cvt, + vector> &cvt, size_t &n_cvt); +bool ReadFile_anno(const string &file_bim, map &mapRS2chr, + map &mapRS2bp, + map &mapRS2cM); +bool ReadFile_pheno(const string &file_pheno, + vector> &indicator_pheno, + vector> &pheno, + const vector &p_column); +bool ReadFile_column(const string &file_pheno, vector &indicator_idv, + vector &pheno, const int &p_column); + +bool ReadFile_geno(const string &file_geno, const set &setSnps, + const gsl_matrix *W, vector &indicator_idv, + vector &indicator_snp, const double &maf_level, + const double &miss_level, const double &hwe_level, + const double &r2_level, map &mapRS2chr, + map &mapRS2bp, + map &mapRS2cM, vector &snpInfo, + size_t &ns_test); +bool ReadFile_bed(const string &file_bed, const set &setSnps, + const gsl_matrix *W, vector &indicator_idv, + vector &indicator_snp, vector &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 &indicator_idv, + igzstream &infile, gsl_vector *geno, double &geno_mean); +void Plink_ReadOneSNP(const int pos, const vector &indicator_idv, + ifstream &infile, gsl_vector *geno, double &geno_mean); + +void ReadFile_kin(const string &file_kin, vector &indicator_idv, + map &mapID2num, const size_t k_mode, bool &error, + gsl_matrix *G); +void ReadFile_mk(const string &file_mk, vector &indicator_idv, + map &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, const set ksnps, + vector &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 &indicator_snp, + const int k_mode, const int display_pace, gsl_matrix *matrix_kin); + +bool ReadFile_geno(const string file_geno, vector &indicator_idv, + vector &indicator_snp, gsl_matrix *UtX, gsl_matrix *K, + const bool calc_K); +bool ReadFile_bed(const string &file_bed, vector &indicator_idv, + vector &indicator_snp, gsl_matrix *UtX, gsl_matrix *K, + const bool calc_K); +bool ReadFile_geno(const string &file_geno, vector &indicator_idv, + vector &indicator_snp, + vector> &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 &indicator_idv, + vector &indicator_snp, vector> &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 &est_column, + map &mapRS2est); + +bool CountFileLines(const string &file_input, size_t &n_lines); + +bool ReadFile_gene(const string &file_gene, vector &vec_read, + vector &snpInfo, size_t &ng_total); + +bool ReadHeader_io(const string &line, HEADER &header); +bool ReadFile_cat(const string &file_cat, map &mapRS2cat, + size_t &n_vc); +bool ReadFile_mcat(const string &file_mcat, map &mapRS2cat, + size_t &n_vc); + +bool ReadFile_catc(const string &file_cat, + map> &mapRS2catc, size_t &n_cat); +bool ReadFile_mcatc(const string &file_mcat, + map> &mapRS2catc, size_t &n_cat); + +bool BimbamKinUncentered(const string &file_geno, const set ksnps, + const int display_pace, + const vector &indicator_idv, + const vector &indicator_snp, + const map &mapRS2weight, + const map &mapRS2cat, + const vector &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 &indicator_idv, + const vector &indicator_snp, + const map &mapRS2weight, + const map &mapRS2cat, + const vector &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 setKSnps, const int display_pace, + const vector &indicator_idv, + const vector> &mindicator_snp, + const map &mapRS2weight, + const map &mapRS2cat, + const vector> &msnpInfo, const gsl_matrix *W, + gsl_matrix *matrix_kin, gsl_vector *vector_ns); + +bool ReadFile_wsnp(const string &file_wsnp, map &mapRS2double); +bool ReadFile_wsnp(const string &file_wcat, const size_t n_vc, + map> &mapRS2vector); + +void ReadFile_beta(const string &file_beta, + const map &mapRS2cat, + const map &mapRS2wA, vector &vec_cat, + vector &vec_ni, vector &vec_weight, + vector &vec_z2, size_t &ni_total, size_t &ns_total, + size_t &ns_test); +void ReadFile_beta(const string &file_beta, const map &mapRS2wA, + map &mapRS2A1, map &mapRS2z); +void Calcq(const size_t n_block, const vector &vec_cat, + const vector &vec_ni, const vector &vec_weight, + const vector &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> &indicator_pheno, + vector> &pheno, + const vector &p_column, vector &indicator_cvt, + vector> &cvt, size_t &n_cvt); + +#endif -- cgit v1.2.3