Merge branch 'master' of github.com:genetics-statistics/GEMMA

1 files changed, 41 insertions, 42 deletions

diff --git a/src/ldr.cpp b/src/ldr.cpp
index f0a1b37..3554efa 100644
--- a/src/ldr.cpp
+++ b/src/ldr.cpp
@@ -16,67 +16,65 @@
  along with this program. If not, see <http://www.gnu.org/licenses/>.
 */
 
-#include <iostream>
 #include <fstream>
+#include <iostream>
 #include <sstream>
 
-#include <iomanip>
+#include <algorithm>
 #include <cmath>
+#include <cstring>
+#include <ctime>
+#include <iomanip>
 #include <iostream>
 #include <stdio.h>
 #include <stdlib.h>
-#include <ctime>
-#include <cstring>
-#include <algorithm>
 
-#include "gsl/gsl_vector.h"
-#include "gsl/gsl_matrix.h"
-#include "gsl/gsl_linalg.h"
+#include "Eigen/Dense"
 #include "gsl/gsl_blas.h"
+#include "gsl/gsl_cdf.h"
 #include "gsl/gsl_eigen.h"
+#include "gsl/gsl_linalg.h"
+#include "gsl/gsl_matrix.h"
 #include "gsl/gsl_randist.h"
-#include "gsl/gsl_cdf.h"
 #include "gsl/gsl_roots.h"
-#include "Eigen/Dense"
+#include "gsl/gsl_vector.h"
 
 #include "lapack.h"
-#include "param.h"
 #include "ldr.h"
 #include "lm.h"
 #include "mathfunc.h"
+#include "param.h"
 
 using namespace std;
 using namespace Eigen;
 
-void LDR::CopyFromParam (PARAM &cPar) {
-	a_mode=cPar.a_mode;
-	d_pace=cPar.d_pace;
+void LDR::CopyFromParam(PARAM &cPar) {
+  a_mode = cPar.a_mode;
+  d_pace = cPar.d_pace;
 
-	file_bfile=cPar.file_bfile;
-	file_geno=cPar.file_geno;
-	file_out=cPar.file_out;
-	path_out=cPar.path_out;
+  file_bfile = cPar.file_bfile;
+  file_geno = cPar.file_geno;
+  file_out = cPar.file_out;
+  path_out = cPar.path_out;
 
-	ni_total=cPar.ni_total;
-	ns_total=cPar.ns_total;
-	ni_test=cPar.ni_test;
-	ns_test=cPar.ns_test;
-	n_cvt=cPar.n_cvt;
+  ni_total = cPar.ni_total;
+  ns_total = cPar.ns_total;
+  ni_test = cPar.ni_test;
+  ns_test = cPar.ns_test;
+  n_cvt = cPar.n_cvt;
 
-	indicator_idv=cPar.indicator_idv;
-	indicator_snp=cPar.indicator_snp;
-	snpInfo=cPar.snpInfo;
+  indicator_idv = cPar.indicator_idv;
+  indicator_snp = cPar.indicator_snp;
+  snpInfo = cPar.snpInfo;
 
-	return;
+  return;
 }
 
-void LDR::CopyToParam (PARAM &cPar) {
-	return;
-}
+void LDR::CopyToParam(PARAM &cPar) { return; }
 
-//X is a p by n matrix.
-void LDR::VB (const vector<vector<unsigned char> > &Xt,
-	      const gsl_matrix *W_gsl, const gsl_vector *y_gsl) {
+// X is a p by n matrix.
+void LDR::VB(const vector<vector<unsigned char>> &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);
@@ -84,20 +82,21 @@ void LDR::VB (const vector<vector<unsigned char> > &Xt,
   VectorXd x_col(y_gsl->size);
 
   double d;
-  for (size_t i=0; i<W_gsl->size1; i++) {
-    d=gsl_vector_get(y_gsl, i);
-    y(i)=d;
-    for (size_t j=0; j<W_gsl->size2; j++) {
-      W(i,j)=gsl_matrix_get(W_gsl, i, j);
+  for (size_t i = 0; i < W_gsl->size1; i++) {
+    d = gsl_vector_get(y_gsl, i);
+    y(i) = d;
+    for (size_t j = 0; j < W_gsl->size2; j++) {
+      W(i, j) = gsl_matrix_get(W_gsl, i, j);
     }
   }
 
   // Initial VB values by lm.
-  cout<<indicator_snp[0]<<" "<<indicator_snp[1]<<" "<<indicator_snp[2]<<endl;
-  uchar_matrix_get_row (Xt, 0, x_col);
+  cout << indicator_snp[0] << " " << indicator_snp[1] << " " << indicator_snp[2]
+       << endl;
+  uchar_matrix_get_row(Xt, 0, x_col);
 
-  for (size_t j=0; j<10; j++) {
-    cout<<x_col(j)<<endl;
+  for (size_t j = 0; j < 10; j++) {
+    cout << x_col(j) << endl;
   }
 
   // Run VB iterations.