version 0.95alpha

1 files changed, 37 insertions, 4 deletions

diff --git a/src/vc.h b/src/vc.h
index f34d72e..d4a9779 100644
--- a/src/vc.h
+++ b/src/vc.h
@@ -16,7 +16,7 @@
     along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
-#ifndef __VC_H__                
+#ifndef __VC_H__
 #define __VC_H__
 
 #include "gsl/gsl_vector.h"
@@ -38,7 +38,7 @@ using namespace std;
 class VC_PARAM
 {
 
-public:	
+public:
 	const gsl_matrix *K;
 	const gsl_matrix *W;
 	const gsl_vector *y;
@@ -47,18 +47,34 @@ public:
 	gsl_matrix *KPy_mat;
 	gsl_matrix *PKPy_mat;
 	gsl_matrix *Hessian;
+	bool noconstrain;
 };
 
 
 
 
+
 class VC {
 
 public:
 	// IO related parameters
+  size_t a_mode;
+	string file_cat;
+	string file_beta;
+	string file_cor;
+	string file_mq;
+	string file_ms;
+
 	string file_out;
 	string path_out;
 
+	set<string> setSnps;
+
+	size_t ni_total_ref, ns_total_ref, ns_pair;
+	size_t ni_total, ns_total, ns_test;
+	size_t n_vc;
+
+	double pve_total, se_pve_total;
 	vector<double> v_sigma2;
 	vector<double> v_se_sigma2;
 	vector<double> v_pve;
@@ -67,16 +83,33 @@ public:
 	vector<double> v_beta;
 	vector<double> v_se_beta;
 
+	size_t crt;
+	double window_cm, window_bp, window_ns;
+
 	double time_UtX;
 	double time_opt;
-	
+
 	// Main functions
 	void CopyFromParam (PARAM &cPar);
 	void CopyToParam (PARAM &cPar);
+	void WriteFile_qs (const gsl_vector *s_vec, const gsl_vector *q_vec, const gsl_vector *qvar_vec, const gsl_matrix *S_mat, const gsl_matrix *Svar_mat);
 	void CalcVChe (const gsl_matrix *K, const gsl_matrix *W, const gsl_vector *y);
-	void CalcVCreml (const gsl_matrix *K, const gsl_matrix *W, const gsl_vector *y);
+	void CalcVCreml (const bool noconstrain, const gsl_matrix *K, const gsl_matrix *W, const gsl_vector *y);
 };
 
+void CalcVCss(const gsl_matrix *Vq, const gsl_matrix *S_mat, const gsl_matrix *Svar_mat, const gsl_vector *q_vec, const gsl_vector *s_vec, const double df, vector<double> &v_pve, vector<double> &v_se_pve, double &pve_total, double &se_pve_total, vector<double> &v_sigma2, vector<double> &v_se_sigma2, vector<double> &v_enrich, vector<double> &v_se_enrich);
+
+
+bool BimbamXwz (const string &file_geno, const int display_pace, vector<int> &indicator_idv, vector<int> &indicator_snp, const vector<size_t> &vec_cat, const gsl_vector *w, const gsl_vector *z, size_t ns_test, gsl_matrix *XWz);
+bool PlinkXwz (const string &file_bed, const int display_pace, vector<int> &indicator_idv, vector<int> &indicator_snp, const vector<size_t> &vec_cat, const gsl_vector *w, const gsl_vector *z, size_t ns_test, gsl_matrix *XWz);
+bool MFILEXwz (const size_t mfile_mode, const string &file_mfile, const int display_pace, vector<int> &indicator_idv, vector<vector<int> > &mindicator_snp, const vector<size_t> &vec_cat, const gsl_vector *w, const gsl_vector *z, gsl_matrix *XWz);
+
+bool BimbamXtXwz (const string &file_geno, const int display_pace, vector<int> &indicator_idv, vector<int> &indicator_snp, const gsl_matrix *XWz, size_t ns_test, gsl_matrix *XtXWz);
+bool PlinkXtXwz (const string &file_bed, const int display_pace, vector<int> &indicator_idv, vector<int> &indicator_snp, const gsl_matrix *XWz, size_t ns_test, gsl_matrix *XtXWz);
+bool MFILEXtXwz (const size_t mfile_mode, const string &file_mfile, const int display_pace, vector<int> &indicator_idv, vector<vector<int> > &mindicator_snp, const gsl_matrix *XWz, gsl_matrix *XtXWz);
+
+void CalcCIss(const gsl_matrix *Xz, const gsl_matrix *XWz, const gsl_matrix *XtXWz, const gsl_matrix *S_mat, const gsl_matrix *Svar_mat, const gsl_vector *w, const gsl_vector *z, const gsl_vector *s_vec, const vector<size_t> &vec_cat, const vector<double> &v_pve, vector<double> &v_se_pve, double &pve_total, double &se_pve_total, vector<double> &v_sigma2, vector<double> &v_se_sigma2, vector<double> &v_enrich, vector<double> &v_se_enrich);
+
 #endif