Updated copyright info

15 files changed, 154 insertions, 50 deletions

diff --git a/src/debug.cpp b/src/debug.cpp
index a4d2562..fd94f1e 100644
--- a/src/debug.cpp
+++ b/src/debug.cpp
@@ -1,3 +1,22 @@
+/*
+    Genome-wide Efficient Mixed Model Association (GEMMA)
+    Copyright © 2011-2017, Xiang Zhou
+    Copyright © 2017, Peter Carbonetto
+    Copyright © 2017, Pjotr Prins
+
+    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/>.
+*/
 
 #include <cmath>
 #include <cstring>
diff --git a/src/debug.h b/src/debug.h
index 0923bd7..208868e 100644
--- a/src/debug.h
+++ b/src/debug.h
@@ -1,3 +1,23 @@
+/*
+    Genome-wide Efficient Mixed Model Association (GEMMA)
+    Copyright © 2011-2017, Xiang Zhou
+    Copyright © 2017, Peter Carbonetto
+    Copyright © 2017, Pjotr Prins
+
+    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 __DEBUG_H__
 #define __DEBUG_H__
 
diff --git a/src/fastblas.cpp b/src/fastblas.cpp
index e971b22..2d9b6e5 100644
--- a/src/fastblas.cpp
+++ b/src/fastblas.cpp
@@ -1,6 +1,8 @@
 /*
     Genome-wide Efficient Mixed Model Association (GEMMA)
-    Copyright (C) 2011-2017, Xiang Zhou
+    Copyright © 2011-2017, Xiang Zhou
+    Copyright © 2017, Peter Carbonetto
+    Copyright © 2017, Pjotr Prins
 
     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
diff --git a/src/fastblas.h b/src/fastblas.h
index d0f5c14..9c5c64c 100644
--- a/src/fastblas.h
+++ b/src/fastblas.h
@@ -1,3 +1,23 @@
+/*
+    Genome-wide Efficient Mixed Model Association (GEMMA)
+    Copyright © 2011-2017, Xiang Zhou
+    Copyright © 2017, Peter Carbonetto
+    Copyright © 2017, Pjotr Prins
+
+    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 __FASTBLAS_H__
 #define __FASTBLAS_H__
 
diff --git a/src/fastopenblas.h b/src/fastopenblas.h
index 969a2e0..3dd8ef7 100644
--- a/src/fastopenblas.h
+++ b/src/fastopenblas.h
@@ -1,3 +1,23 @@
+/*
+    Genome-wide Efficient Mixed Model Association (GEMMA)
+    Copyright © 2011-2017, Xiang Zhou
+    Copyright © 2017, Peter Carbonetto
+    Copyright © 2017, Pjotr Prins
+
+    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 __FASTOPENBLAS_H__
 #define __FASTOPENBLAS_H__
 
diff --git a/src/gemma.cpp b/src/gemma.cpp
index 39402b5..e31eaed 100644
--- a/src/gemma.cpp
+++ b/src/gemma.cpp
@@ -1,6 +1,8 @@
 /*
     Genome-wide Efficient Mixed Model Association (GEMMA)
-    Copyright (C) 2011-2017, Xiang Zhou
+    Copyright © 2011-2017, Xiang Zhou
+    Copyright © 2017, Peter Carbonetto
+    Copyright © 2017, Pjotr Prins
 
     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
@@ -78,9 +80,7 @@ void gemma_gsl_error_handler (const char * reason,
 void GEMMA::PrintHeader(void) {
 
   cout <<
-    "GEMMA " << version << " (" << date << ") by Xiang Zhou et al. (C) 2012-" << year << endl;
-  cout <<
-    "   http://www.xzlab.org/software.html, https://github.com/genetics-statistics" << endl;
+    "GEMMA " << version << " (" << date << ") by Xiang Zhou and team (C) 2012-" << year << endl;
   return;
 }
 
@@ -149,19 +149,20 @@ void GEMMA::PrintLicense(void) {
 }
 
 void GEMMA::PrintHelp(size_t option) {
+
   if (option == 0) {
     cout << endl;
-    cout << " type ./gemma -h [num] for detailed helps" << endl;
+    cout << " type ./gemma -h [num] for detailed help" << endl;
     cout << " options: " << endl;
-    cout << " 1: quick guide" << endl;
-    cout << " 2: file I/O related" << endl;
-    cout << " 3: SNP QC" << endl;
-    cout << " 4: calculate relatedness matrix" << endl;
-    cout << " 5: perform eigen decomposition" << endl;
-    cout << " 6: perform variance component estimation" << endl;
-    cout << " 7: fit a linear model" << endl;
-    cout << " 8: fit a linear mixed model" << endl;
-    cout << " 9: fit a multivariate linear mixed model" << endl;
+    cout << "  1: quick guide" << endl;
+    cout << "  2: file I/O related" << endl;
+    cout << "  3: SNP QC" << endl;
+    cout << "  4: calculate relatedness matrix" << endl;
+    cout << "  5: perform eigen decomposition" << endl;
+    cout << "  6: perform variance component estimation" << endl;
+    cout << "  7: fit a linear model" << endl;
+    cout << "  8: fit a linear mixed model" << endl;
+    cout << "  9: fit a multivariate linear mixed model" << endl;
     cout << " 10: fit a Bayesian sparse linear mixed model" << endl;
     cout << " 11: obtain predicted values" << endl;
     cout << " 12: calculate snp variance covariance" << endl;
@@ -719,6 +720,10 @@ void GEMMA::PrintHelp(size_t option) {
     cout << endl;
   }
 
+  cout << "The GEMMA software is distributed under the GNU General Public v3" << endl;
+  cout << "   -license    show license information" << endl;
+  cout <<
+    "   see also http://www.xzlab.org/software.html, https://github.com/genetics-statistics" << endl;
   return;
 }
 
diff --git a/src/gemma.h b/src/gemma.h
index cd1683a..4deab51 100644
--- a/src/gemma.h
+++ b/src/gemma.h
@@ -1,6 +1,8 @@
 /*
     Genome-wide Efficient Mixed Model Association (GEMMA)
-    Copyright (C) 2011-2017, Xiang Zhou
+    Copyright © 2011-2017, Xiang Zhou
+    Copyright © 2017, Peter Carbonetto
+    Copyright © 2017, Pjotr Prins
 
     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
diff --git a/src/io.cpp b/src/io.cpp
index 625a6a2..5c48aa6 100644
--- a/src/io.cpp
+++ b/src/io.cpp
@@ -1,6 +1,8 @@
 /*
     Genome-wide Efficient Mixed Model Association (GEMMA)
-    Copyright (C) 2011-2017, Xiang Zhou
+    Copyright © 2011-2017, Xiang Zhou
+    Copyright © 2017, Peter Carbonetto
+    Copyright © 2017, Pjotr Prins
 
     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
diff --git a/src/io.h b/src/io.h
index 215e8ba..dd1d5c0 100644
--- a/src/io.h
+++ b/src/io.h
@@ -1,6 +1,8 @@
 /*
     Genome-wide Efficient Mixed Model Association (GEMMA)
-    Copyright (C) 2011-2017, Xiang Zhou
+    Copyright © 2011-2017, Xiang Zhou
+    Copyright © 2017, Peter Carbonetto
+    Copyright © 2017, Pjotr Prins
 
     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
diff --git a/src/lmm.cpp b/src/lmm.cpp
index 91354e1..4198fab 100644
--- a/src/lmm.cpp
+++ b/src/lmm.cpp
@@ -1,6 +1,8 @@
 /*
     Genome-wide Efficient Mixed Model Association (GEMMA)
-    Copyright (C) 2011-2017, Xiang Zhou
+    Copyright © 2011-2017, Xiang Zhou
+    Copyright © 2017, Peter Carbonetto
+    Copyright © 2017, Pjotr Prins
 
     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
@@ -13,7 +15,7 @@
     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/>.
+    along with this program. If not, see <http://www.gnu.org/licenses/>.
 */
 
 #include <fstream>
diff --git a/src/lmm.h b/src/lmm.h
index 9c46fae..e9740d5 100644
--- a/src/lmm.h
+++ b/src/lmm.h
@@ -1,6 +1,8 @@
 /*
     Genome-wide Efficient Mixed Model Association (GEMMA)
-    Copyright (C) 2011-2017, Xiang Zhou
+    Copyright © 2011-2017, Xiang Zhou
+    Copyright © 2017, Peter Carbonetto
+    Copyright © 2017, Pjotr Prins
 
     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
diff --git a/src/mathfunc.cpp b/src/mathfunc.cpp
index 2cce43f..9076c47 100644
--- a/src/mathfunc.cpp
+++ b/src/mathfunc.cpp
@@ -1,19 +1,21 @@
 /*
- Genome-wide Efficient Mixed Model Association (GEMMA)
- 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
- 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/>.
+    Genome-wide Efficient Mixed Model Association (GEMMA)
+    Copyright © 2011-2017, Xiang Zhou
+    Copyright © 2017, Peter Carbonetto
+    Copyright © 2017, Pjotr Prins
+
+    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/>.
 */
 
 #include <bitset>
diff --git a/src/mathfunc.h b/src/mathfunc.h
index 481d022..8258c22 100644
--- a/src/mathfunc.h
+++ b/src/mathfunc.h
@@ -1,19 +1,21 @@
 /*
- Genome-wide Efficient Mixed Model Association (GEMMA)
- Copyright (C) 2011-2017, Xiang Zhou
+    Genome-wide Efficient Mixed Model Association (GEMMA)
+    Copyright © 2011-2017, Xiang Zhou
+    Copyright © 2017, Peter Carbonetto
+    Copyright © 2017, Pjotr Prins
 
- 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 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.
+    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/>.
+    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 __MATHFUNC_H__
diff --git a/src/param.cpp b/src/param.cpp
index 4ae5adf..bf6c195 100644
--- a/src/param.cpp
+++ b/src/param.cpp
@@ -1,6 +1,8 @@
 /*
     Genome-wide Efficient Mixed Model Association (GEMMA)
-    Copyright (C) 2011-2017, Xiang Zhou
+    Copyright © 2011-2017, Xiang Zhou
+    Copyright © 2017, Peter Carbonetto
+    Copyright © 2017, Pjotr Prins
 
     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
diff --git a/src/param.h b/src/param.h
index 0199d59..9ad14b2 100644
--- a/src/param.h
+++ b/src/param.h
@@ -1,6 +1,8 @@
 /*
     Genome-wide Efficient Mixed Model Association (GEMMA)
-    Copyright (C) 2011-2017, Xiang Zhou
+    Copyright © 2011-2017, Xiang Zhou
+    Copyright © 2017, Peter Carbonetto
+    Copyright © 2017, Pjotr Prins
 
     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