Merge pull request #70 from genenetwork/issue14

Fixes output file with kinship has extra column.

4 files changed, 16 insertions, 14 deletions

diff --git a/src/gemma.cpp b/src/gemma.cpp
index 3197043..c82bf4a 100644
--- a/src/gemma.cpp
+++ b/src/gemma.cpp
@@ -1789,14 +1789,14 @@ void GEMMA::BatchRun(PARAM &cPar) {
       cout << "REMLE estimate for Vg in the null model: " << endl;
       for (size_t i = 0; i < Vg->size1; i++) {
         for (size_t j = 0; j <= i; j++) {
-          cout << gsl_matrix_get(Vg, i, j) << "\t";
+          cout << tab(j) << gsl_matrix_get(Vg, i, j);
         }
         cout << endl;
       }
       cout << "REMLE estimate for Ve in the null model: " << endl;
       for (size_t i = 0; i < Ve->size1; i++) {
         for (size_t j = 0; j <= i; j++) {
-          cout << gsl_matrix_get(Ve, i, j) << "\t";
+          cout << tab(j) << gsl_matrix_get(Ve, i, j);
         }
         cout << endl;
       }
@@ -3560,7 +3560,7 @@ void GEMMA::WriteLog(int argc, char **argv, PARAM &cPar) {
         for (size_t j = 0; j <= i; j++) {
           c = (2 * cPar.n_ph - min(i, j) + 1) * min(i, j) / 2 + max(i, j) -
               min(i, j);
-          outfile << cPar.Vg_remle_null[c] << "\t";
+          outfile << tab(j) << cPar.Vg_remle_null[c];
         }
         outfile << endl;
       }
@@ -3569,7 +3569,7 @@ void GEMMA::WriteLog(int argc, char **argv, PARAM &cPar) {
         for (size_t j = 0; j <= i; j++) {
           c = (2 * cPar.n_ph - min(i, j) + 1) * min(i, j) / 2 + max(i, j) -
               min(i, j);
-          outfile << sqrt(cPar.VVg_remle_null[c]) << "\t";
+          outfile << tab(j) << sqrt(cPar.VVg_remle_null[c]);
         }
         outfile << endl;
       }
@@ -3578,7 +3578,7 @@ void GEMMA::WriteLog(int argc, char **argv, PARAM &cPar) {
         for (size_t j = 0; j <= i; j++) {
           c = (2 * cPar.n_ph - min(i, j) + 1) * min(i, j) / 2 + max(i, j) -
               min(i, j);
-          outfile << cPar.Ve_remle_null[c] << "\t";
+          outfile << tab(j) << cPar.Ve_remle_null[c];
         }
         outfile << endl;
       }
@@ -3587,7 +3587,7 @@ void GEMMA::WriteLog(int argc, char **argv, PARAM &cPar) {
         for (size_t j = 0; j <= i; j++) {
           c = (2 * cPar.n_ph - min(i, j) + 1) * min(i, j) / 2 + max(i, j) -
               min(i, j);
-          outfile << sqrt(cPar.VVe_remle_null[c]) << "\t";
+          outfile << tab(j) << sqrt(cPar.VVe_remle_null[c]);
         }
         outfile << endl;
       }
@@ -3597,7 +3597,7 @@ void GEMMA::WriteLog(int argc, char **argv, PARAM &cPar) {
         for (size_t j = 0; j < cPar.n_ph; j++) {
           c = (2 * cPar.n_ph - min(i, j) + 1) * min(i, j) / 2 + max(i, j) -
               min(i, j);
-          outfile << cPar.Vg_mle_null[c] << "\t";
+          outfile << tab(j) << cPar.Vg_mle_null[c];
         }
         outfile << endl;
       }
@@ -3606,7 +3606,7 @@ void GEMMA::WriteLog(int argc, char **argv, PARAM &cPar) {
         for (size_t j = 0; j <= i; j++) {
           c = (2 * cPar.n_ph - min(i, j) + 1) * min(i, j) / 2 + max(i, j) -
               min(i, j);
-          outfile << sqrt(cPar.VVg_mle_null[c]) << "\t";
+          outfile << tab(j) << sqrt(cPar.VVg_mle_null[c]);
         }
         outfile << endl;
       }
@@ -3615,7 +3615,7 @@ void GEMMA::WriteLog(int argc, char **argv, PARAM &cPar) {
         for (size_t j = 0; j < cPar.n_ph; j++) {
           c = (2 * cPar.n_ph - min(i, j) + 1) * min(i, j) / 2 + max(i, j) -
               min(i, j);
-          outfile << cPar.Ve_mle_null[c] << "\t";
+          outfile << tab(j) << cPar.Ve_mle_null[c];
         }
         outfile << endl;
       }
@@ -3624,7 +3624,7 @@ void GEMMA::WriteLog(int argc, char **argv, PARAM &cPar) {
         for (size_t j = 0; j <= i; j++) {
           c = (2 * cPar.n_ph - min(i, j) + 1) * min(i, j) / 2 + max(i, j) -
               min(i, j);
-          outfile << sqrt(cPar.VVe_mle_null[c]) << "\t";
+          outfile << tab(j) << sqrt(cPar.VVe_mle_null[c]);
         }
         outfile << endl;
       }
@@ -3634,7 +3634,7 @@ void GEMMA::WriteLog(int argc, char **argv, PARAM &cPar) {
       for (size_t i = 0; i < cPar.n_ph; i++) {
         for (size_t j = 0; j < cPar.n_cvt; j++) {
           c = i * cPar.n_cvt + j;
-          outfile << cPar.beta_remle_null[c] << "\t";
+          outfile << tab(j) << cPar.beta_remle_null[c];
         }
         outfile << endl;
       }
@@ -3642,7 +3642,7 @@ void GEMMA::WriteLog(int argc, char **argv, PARAM &cPar) {
       for (size_t i = 0; i < cPar.n_ph; i++) {
         for (size_t j = 0; j < cPar.n_cvt; j++) {
           c = i * cPar.n_cvt + j;
-          outfile << cPar.se_beta_remle_null[c] << "\t";
+          outfile << tab(j) << cPar.se_beta_remle_null[c];
         }
         outfile << endl;
       }
diff --git a/src/io.cpp b/src/io.cpp
index 79e753a..8f3b58f 100644
--- a/src/io.cpp
+++ b/src/io.cpp
@@ -1162,7 +1162,7 @@ void ReadFile_kin(const string &file_kin, vector<int> &indicator_idv,
     }
     if (i_total != ni_total) {
       cout << "error! number of rows in the kinship file do "
-           << "not match the number of phentypes." << endl;
+           << "not match the number of phenotypes." << endl;
       error = true;
     }
   } else {
diff --git a/src/io.h b/src/io.h
index 27f145f..9edc5eb 100644
--- a/src/io.h
+++ b/src/io.h
@@ -28,6 +28,8 @@
 #include "gzstream.h"
 #include "param.h"
 
+#define tab(col) ( col ? "\t" : "")
+
 using namespace std;
 
 void ProgressBar(string str, double p, double total);
diff --git a/src/param.cpp b/src/param.cpp
index 6ab4339..d1879d1 100644
--- a/src/param.cpp
+++ b/src/param.cpp
@@ -1955,7 +1955,7 @@ void PARAM::WriteMatrix(const gsl_matrix *matrix_U, const string suffix) {
 
   for (size_t i = 0; i < matrix_U->size1; ++i) {
     for (size_t j = 0; j < matrix_U->size2; ++j) {
-      outfile << gsl_matrix_get(matrix_U, i, j) << "\t";
+      outfile << tab(j) << gsl_matrix_get(matrix_U, i, j);
     }
     outfile << endl;
   }