From c22801f32c3c459997041fb9ad27bd0ab5de372c Mon Sep 17 00:00:00 2001 From: Peter Carbonetto Date: Thu, 1 Jun 2017 17:27:50 -0500 Subject: Removed FORCE_FLOAT from additional C++ source files. --- src/bslmm.cpp | 2 +- src/bslmm.h | 5 +- src/bslmmdap.cpp | 4 +- src/bslmmdap.h | 4 +- src/eigenlib.h | 2 +- src/gzstream.h | 3 +- src/lapack.h | 2 +- src/ldr.cpp | 207 +++++-------------------------------------------------- src/ldr.h | 50 ++++++-------- src/main.cpp | 24 ++----- src/varcov.cpp | 6 +- src/varcov.h | 6 +- 12 files changed, 59 insertions(+), 256 deletions(-) (limited to 'src') diff --git a/src/bslmm.cpp b/src/bslmm.cpp index 0bd4234..d295fd8 100644 --- a/src/bslmm.cpp +++ b/src/bslmm.cpp @@ -1,6 +1,6 @@ /* Genome-wide Efficient Mixed Model Association (GEMMA) - Copyright (C) 2011-2017 Xiang Zhou + 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 diff --git a/src/bslmm.h b/src/bslmm.h index 863a22d..07aac67 100644 --- a/src/bslmm.h +++ b/src/bslmm.h @@ -1,6 +1,6 @@ /* Genome-wide Efficient Mixed Model Association (GEMMA) - Copyright (C) 2011-2017 Xiang Zhou + 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 @@ -14,8 +14,7 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . - */ - +*/ #ifndef __BSLMM_H__ #define __BSLMM_H__ diff --git a/src/bslmmdap.cpp b/src/bslmmdap.cpp index c66189b..e1b20d8 100644 --- a/src/bslmmdap.cpp +++ b/src/bslmmdap.cpp @@ -1,6 +1,6 @@ /* Genome-wide Efficient Mixed Model Association (GEMMA) - Copyright (C) 2011-2017 Xiang Zhou + 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 @@ -14,7 +14,7 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . - */ +*/ #include #include diff --git a/src/bslmmdap.h b/src/bslmmdap.h index a9e2d51..7d95db7 100644 --- a/src/bslmmdap.h +++ b/src/bslmmdap.h @@ -1,6 +1,6 @@ /* Genome-wide Efficient Mixed Model Association (GEMMA) - Copyright (C) 2011-2017 Xiang Zhou + 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 @@ -14,7 +14,7 @@ You should have received a copy of the GNU General Public License along with this program. If not, see . - */ +*/ #ifndef __BSLMMDAP_H__ #define __BSLMMDAP_H__ diff --git a/src/eigenlib.h b/src/eigenlib.h index 493907c..f869786 100644 --- a/src/eigenlib.h +++ b/src/eigenlib.h @@ -1,6 +1,6 @@ /* Genome-wide Efficient Mixed Model Association (GEMMA) - Copyright (C) 2011-2017 Xiang Zhou + 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 diff --git a/src/gzstream.h b/src/gzstream.h index 861653f..4e86ad9 100644 --- a/src/gzstream.h +++ b/src/gzstream.h @@ -29,7 +29,7 @@ #ifndef GZSTREAM_H #define GZSTREAM_H 1 -// standard C++ with new header file names and std:: namespace +// Standard C++ with new header file names and std::namespace. #include #include #include @@ -118,4 +118,3 @@ public: #endif // GZSTREAM_H // ============================================================================ // EOF // - diff --git a/src/lapack.h b/src/lapack.h index 5277b2f..88fc509 100644 --- a/src/lapack.h +++ b/src/lapack.h @@ -1,6 +1,6 @@ /* Genome-wide Efficient Mixed Model Association (GEMMA) - Copyright (C) 2011-2017 Xiang Zhou + 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 diff --git a/src/ldr.cpp b/src/ldr.cpp index e28490a..a1e5791 100644 --- a/src/ldr.cpp +++ b/src/ldr.cpp @@ -1,6 +1,6 @@ /* Genome-wide Efficient Mixed Model Association (GEMMA) - Copyright (C) 2011 Xiang Zhou + 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 @@ -13,8 +13,8 @@ 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 . - */ + along with this program. If not, see . +*/ #include #include @@ -39,29 +39,16 @@ #include "gsl/gsl_roots.h" #include "Eigen/Dense" - - #include "lapack.h" - -#ifdef FORCE_FLOAT -#include "param_float.h" -#include "ldr_float.h" -#include "lm_float.h" -#include "mathfunc_float.h" //for function CenterVector -#else #include "param.h" #include "ldr.h" #include "lm.h" #include "mathfunc.h" -#endif using namespace std; using namespace Eigen; - - -void LDR::CopyFromParam (PARAM &cPar) -{ +void LDR::CopyFromParam (PARAM &cPar) { a_mode=cPar.a_mode; d_pace=cPar.d_pace; @@ -83,176 +70,15 @@ void LDR::CopyFromParam (PARAM &cPar) return; } - -void LDR::CopyToParam (PARAM &cPar) -{ - //cPar.pheno_mean=pheno_mean; - //cPar.randseed=randseed; - - return; -} - - -/* -void BSLMM::WriteBV (const gsl_vector *bv) -{ - string file_str; - file_str=path_out+"/"+file_out; - file_str+=".bv.txt"; - - ofstream outfile (file_str.c_str(), ofstream::out); - if (!outfile) {cout<<"error writing file: "< > &beta_g, const gsl_vector *alpha, const size_t w) -{ - string file_str; - file_str=path_out+"/"+file_out; - file_str+=".param.txt"; - - ofstream outfile (file_str.c_str(), ofstream::out); - if (!outfile) {cout<<"error writing file: "< > &Xt, const gsl_matrix *W_gsl, const gsl_vector *y_gsl) -{ - //save gsl_vector and gsl_matrix into eigen library formats +//X is a p by n matrix. +void LDR::VB (const vector > &Xt, + const gsl_matrix *W_gsl, const gsl_vector *y_gsl) { + + // Save gsl_vector and gsl_matrix into Eigen library formats. MatrixXd W(W_gsl->size1, W_gsl->size2); VectorXd y(y_gsl->size); VectorXd x_col(y_gsl->size); @@ -266,7 +92,7 @@ void LDR::VB (const vector > &Xt, const gsl_matrix *W_gsl, } } - //initial VB values by lm + // Initial VB values by lm. cout< > &Xt, const gsl_matrix *W_gsl, cout<. - */ - + along with this program. If not, see . +*/ #ifndef __LDR_H__ #define __LDR_H__ @@ -24,25 +23,14 @@ #include #include #include - -#ifdef FORCE_FLOAT -#include "param_float.h" -#else #include "param.h" -#endif - using namespace std; - - - - - class LDR { public: - // IO related parameters + // IO-related parameters. int a_mode; size_t d_pace; @@ -51,27 +39,33 @@ public: string file_out; string path_out; - // Summary statistics - size_t ni_total, ns_total; //number of total individuals and snps - size_t ni_test, ns_test; //number of individuals and snps used for analysis - size_t n_cvt; //number of covariates - vector indicator_idv; //indicator for individuals (phenotypes), 0 missing, 1 available for analysis - vector indicator_snp; //sequence indicator for SNPs: 0 ignored because of (a) maf, (b) miss, (c) non-poly; 1 available for analysis + // Summary statistics. + size_t ni_total, ns_total; // Total number of individuals & SNPs. + size_t ni_test, ns_test; // Number of individuals & SNPs used + // for analysis + size_t n_cvt; // Number of covariates. + + // Indicator for individuals (phenotypes): 0 missing, 1 + // available for analysis. + vector indicator_idv; + + // Sequence indicator for SNPs: 0 ignored because of (a) maf, + // (b) miss, (c) non-poly; 1 available for analysis. + vector indicator_snp; - vector snpInfo; //record SNP information + vector snpInfo; // Record SNP information. - // Not included in PARAM + // Not included in PARAM. gsl_rng *gsl_r; - // Main Functions + // Main functions. void CopyFromParam (PARAM &cPar); void CopyToParam (PARAM &cPar); - void VB(const vector > &Xt, const gsl_matrix *W_gsl, const gsl_vector *y_gsl); + void VB(const vector > &Xt, + const gsl_matrix *W_gsl, const gsl_vector *y_gsl); }; - - #endif diff --git a/src/main.cpp b/src/main.cpp index e1fb336..b7ac884 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -1,6 +1,6 @@ /* - Genome-wide Efficient Mixed Model Association (GEMMA) - Copyright (C) 2011 Xiang Zhou + 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 @@ -13,7 +13,7 @@ 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 . + along with this program. If not, see . */ #include @@ -21,21 +21,11 @@ #include #include #include - -#include "param.h" - -#ifdef FORCE_FLOAT -#include "gemma_float.h" -#else #include "gemma.h" -#endif using namespace std; - - -int main(int argc, char * argv[]) -{ +int main(int argc, char * argv[]) { GEMMA cGemma; PARAM cPar; @@ -79,8 +69,4 @@ int main(int argc, char * argv[]) cGemma.WriteLog(argc, argv, cPar); - return EXIT_SUCCESS; -} - - - + return EXIT_SUCCESS; } diff --git a/src/varcov.cpp b/src/varcov.cpp index 66cf3c4..9d39c6c 100644 --- a/src/varcov.cpp +++ b/src/varcov.cpp @@ -1,6 +1,6 @@ /* - Genome-wide Efficient Mixed Model Association (GEMMA) - Copyright (C) 2011-2017 Xiang Zhou + 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 @@ -13,7 +13,7 @@ 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 . + along with this program. If not, see . */ #include diff --git a/src/varcov.h b/src/varcov.h index a7fcd9c..291f16c 100644 --- a/src/varcov.h +++ b/src/varcov.h @@ -1,6 +1,6 @@ /* - Genome-wide Efficient Mixed Model Association (GEMMA) - Copyright (C) 2011-2017 Xiang Zhou + 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 @@ -13,7 +13,7 @@ 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 . + along with this program. If not, see . */ #ifndef __VARCOV_H__ -- cgit v1.2.3