From bfe06c298c1b9e8be12df91e4f1c9a8e5c459562 Mon Sep 17 00:00:00 2001
From: Peter Carbonetto
Date: Fri, 2 Jun 2017 00:07:12 -0500
Subject: Removed FORCE_FLOAT from lmm.h,cpp.
---
src/lm.h | 54 +++++++++++++++++++++++++++---------------------------
1 file changed, 27 insertions(+), 27 deletions(-)
(limited to 'src/lm.h')
diff --git a/src/lm.h b/src/lm.h
index 656dd52..fac84e1 100644
--- a/src/lm.h
+++ b/src/lm.h
@@ -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
@@ -13,33 +13,25 @@
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 __LM_H__
#define __LM_H__
#include "gsl/gsl_vector.h"
#include "gsl/gsl_matrix.h"
-
-
-#ifdef FORCE_FLOAT
-#include "param_float.h"
-#include "io_float.h"
-#else
#include "param.h"
#include "io.h"
-#endif
using namespace std;
-
class LM {
public:
- // IO related parameters
- int a_mode; //analysis mode, 50+1/2/3/4 for Frequentist tests
- size_t d_pace; //display pace
+ // IO-related parameters.
+ int a_mode; // Analysis mode: 50+1/2/3/4 for Frequentist tests.
+ size_t d_pace; // Display pace.
string file_bfile;
string file_geno;
@@ -49,31 +41,39 @@ public:
string file_gene;
- // Summary statistics
- size_t ni_total, ni_test; //number of individuals
- size_t ns_total, ns_test; //number of snps
- size_t ng_total, ng_test; //number of genes
+ // Summary statistics.
+ size_t ni_total, ni_test; // Number of individuals.
+ size_t ns_total, ns_test; // Number of SNPs.
+ size_t ng_total, ng_test; // Number of genes.
size_t n_cvt;
- double time_opt; //time spent
+ double time_opt; // Time spent.
- 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
+ // Indicator for individuals (phenotypes): 0 missing, 1
+ // available for analysis.
+ vector indicator_idv;
- vector snpInfo; //record SNP information
+ // Sequence indicator for SNPs: 0 ignored because of (a) maf,
+ // (b) miss, (c) non-poly; 1 available for analysis.
+ vector indicator_snp;
- // Not included in PARAM
- vector sumStat; //Output SNPSummary Data
+ vector snpInfo; // Record SNP information.
- // Main functions
+ // Not included in PARAM.
+ vector sumStat; // Output SNPSummary Data.
+
+ // Main functions.
void CopyFromParam (PARAM &cPar);
void CopyToParam (PARAM &cPar);
void AnalyzeGene (const gsl_matrix *W, const gsl_vector *x);
void AnalyzePlink (const gsl_matrix *W, const gsl_vector *y);
void AnalyzeBimbam (const gsl_matrix *W, const gsl_vector *y);
- // WJA added
+ // WJA added.
void Analyzebgen (const gsl_matrix *W, const gsl_vector *y);
void WriteFiles ();
};
-void MatrixCalcLmLR (const gsl_matrix *X, const gsl_vector *y, vector > &pos_loglr);
+
+void MatrixCalcLmLR (const gsl_matrix *X, const gsl_vector *y,
+ vector > &pos_loglr);
+
#endif
--
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