add GXE test

1 files changed, 16 insertions, 12 deletions

diff --git a/src/lm.h b/src/lm.h
index ceec060..656dd52 100644
--- a/src/lm.h
+++ b/src/lm.h
@@ -1,22 +1,22 @@
 /*
  Genome-wide Efficient Mixed Model Association (GEMMA)
  Copyright (C) 2011  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 __LM_H__                
+#ifndef __LM_H__
 #define __LM_H__
 
 #include "gsl/gsl_vector.h"
@@ -35,40 +35,44 @@ 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
-	
+
 	string file_bfile;
 	string file_geno;
+	string file_oxford;
 	string file_out;
 	string path_out;
-	
+
 	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
 	size_t n_cvt;
 	double time_opt;		//time spent
-	
+
 	vector<int> indicator_idv;				//indicator for individuals (phenotypes), 0 missing, 1 available for analysis
 	vector<int> indicator_snp;				//sequence indicator for SNPs: 0 ignored because of (a) maf, (b) miss, (c) non-poly; 1 available for analysis
-	
+
 	vector<SNPINFO> snpInfo;		//record SNP information
-	
+
 	// Not included in PARAM
 	vector<SUMSTAT> 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
+	void Analyzebgen (const gsl_matrix *W, const gsl_vector *y);
+
 	void WriteFiles ();
 };
 void MatrixCalcLmLR (const gsl_matrix *X, const gsl_vector *y, vector<pair<size_t, double> > &pos_loglr);