[Genabel-commits] r1604 - in branches/ProbABEL-0.50: . doc src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Feb 10 23:29:48 CET 2014
Author: maartenk
Date: 2014-02-10 23:29:48 +0100 (Mon, 10 Feb 2014)
New Revision: 1604
Modified:
branches/ProbABEL-0.50/configure.ac
branches/ProbABEL-0.50/doc/ChangeLog
branches/ProbABEL-0.50/doc/ProbABEL_manual.tex
branches/ProbABEL-0.50/doc/README.dox
branches/ProbABEL-0.50/doc/pacoxph.1
branches/ProbABEL-0.50/doc/palinear.1
branches/ProbABEL-0.50/doc/palogist.1
branches/ProbABEL-0.50/doc/probabel.1
branches/ProbABEL-0.50/src/command_line_settings.cpp
branches/ProbABEL-0.50/src/command_line_settings.h
branches/ProbABEL-0.50/src/coxph_data.cpp
branches/ProbABEL-0.50/src/coxph_data.h
branches/ProbABEL-0.50/src/data.cpp
branches/ProbABEL-0.50/src/data.h
branches/ProbABEL-0.50/src/eigen_mematrix.cpp
branches/ProbABEL-0.50/src/eigen_mematrix.h
branches/ProbABEL-0.50/src/gendata.cpp
branches/ProbABEL-0.50/src/gendata.h
branches/ProbABEL-0.50/src/main.cpp
branches/ProbABEL-0.50/src/main_functions_dump.cpp
branches/ProbABEL-0.50/src/main_functions_dump.h
branches/ProbABEL-0.50/src/maskedmatrix.cpp
branches/ProbABEL-0.50/src/maskedmatrix.h
branches/ProbABEL-0.50/src/mematri1.h
branches/ProbABEL-0.50/src/mematrix.h
branches/ProbABEL-0.50/src/phedata.cpp
branches/ProbABEL-0.50/src/phedata.h
branches/ProbABEL-0.50/src/reg1.cpp
branches/ProbABEL-0.50/src/reg1.h
branches/ProbABEL-0.50/src/regdata.cpp
branches/ProbABEL-0.50/src/regdata.h
branches/ProbABEL-0.50/src/testchol.cpp
branches/ProbABEL-0.50/src/usage.cpp
branches/ProbABEL-0.50/src/usage.h
branches/ProbABEL-0.50/src/utilities.cpp
branches/ProbABEL-0.50/src/utilities.h
Log:
Updated ProbABEL-0.50 branch to probabel trunk
Modified: branches/ProbABEL-0.50/configure.ac
===================================================================
--- branches/ProbABEL-0.50/configure.ac 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/configure.ac 2014-02-10 22:29:48 UTC (rev 1604)
@@ -2,7 +2,7 @@
# Process this file with autoconf to produce a configure script.
AC_PREREQ([2.67])
-AC_INIT(ProbABEL, 0.4.2, genabel-devel at r-forge.wu-wien.ac.at)
+AC_INIT(ProbABEL, 0.4.3, genabel-devel at r-forge.wu-wien.ac.at)
AM_INIT_AUTOMAKE([silent-rules subdir-objects])
AM_SILENT_RULES([yes])
AC_CONFIG_SRCDIR([src/data.h])
Modified: branches/ProbABEL-0.50/doc/ChangeLog
===================================================================
--- branches/ProbABEL-0.50/doc/ChangeLog 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/doc/ChangeLog 2014-02-10 22:29:48 UTC (rev 1604)
@@ -1,3 +1,7 @@
+***** v.0.4.3
+* Speed up of a factor of X after simplifying the way filevector data is
+ read in.
+
***** v.0.4.2
* The 'probabel.pl' script is now simply renamed to 'probabel' (a user
shouldn't care what scripting language we use). For at least several
Modified: branches/ProbABEL-0.50/doc/ProbABEL_manual.tex
===================================================================
--- branches/ProbABEL-0.50/doc/ProbABEL_manual.tex 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/doc/ProbABEL_manual.tex 2014-02-10 22:29:48 UTC (rev 1604)
@@ -1,6 +1,6 @@
\documentclass[12pt,a4paper]{article}
-\title{Manual for ProbABEL v0.4.2}
+\title{Manual for ProbABEL v0.4.3}
\author{\emph{Current Programmers:} Lennart Karssen$^{1,2}$, Maarten
Kooyman$^2$, \\
Yurii Aulchenko$^{1,3}$ \\
@@ -11,7 +11,7 @@
$^{2}${\small Erasmus MC, Rotterdam}\\
$^{3}${\small Institute of Cytology and Genetics SD RAS, Novosibirsk}
}
-\date{January 2, 2014}
+\date{January 30, 2014}
\usepackage{verbatim}
\usepackage{titleref}
@@ -295,7 +295,7 @@
short explanation to the command line options:
\begin{verbatim}
user at server:~$ palogist --help
-probabel v. 0.4.2
+probabel v. 0.4.3
(C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR
Using EIGEN version 3.1.2 for matrix operations
@@ -855,7 +855,7 @@
\end{quote}
A proper reference may look like
\begin{quote}
-For the analysis of imputed data, we used the \PA{} v.0.4.2
+For the analysis of imputed data, we used \PA{} v.0.4.3
from the \texttt{GenABEL} suite of programs (Aulchenko \emph{et al.}, 2010).
\end{quote}
Modified: branches/ProbABEL-0.50/doc/README.dox
===================================================================
--- branches/ProbABEL-0.50/doc/README.dox 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/doc/README.dox 2014-02-10 22:29:48 UTC (rev 1604)
@@ -6,6 +6,8 @@
\author L.C. Karssen
\author M. Kooyman
\author Maksim V. Struchalin
+\author Other members of the GenABEL team
+\author People who submitted patches to the mailing list or bug tracker
The ProbABEL package is part of the GenABEL project for analysis of genome-wide
data. ProbABEL is used to run GWAS. Using files in filevector/DatABEL format
Modified: branches/ProbABEL-0.50/doc/pacoxph.1
===================================================================
--- branches/ProbABEL-0.50/doc/pacoxph.1 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/doc/pacoxph.1 2014-02-10 22:29:48 UTC (rev 1604)
@@ -1,4 +1,4 @@
-.TH pacoxph 1 "2 January 2014" "ProbABEL 0.4.2"
+.TH pacoxph 1 "2 January 2014" "ProbABEL 0.4.3"
.SH NAME
pacoxph \- Perform Genome-Wide Association Analysis using a linear model
.SH SYNOPSIS
Modified: branches/ProbABEL-0.50/doc/palinear.1
===================================================================
--- branches/ProbABEL-0.50/doc/palinear.1 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/doc/palinear.1 2014-02-10 22:29:48 UTC (rev 1604)
@@ -1,4 +1,4 @@
-.TH palinear 1 "2 January 2014" "ProbABEL 0.4.2"
+.TH palinear 1 "2 January 2014" "ProbABEL 0.4.3"
.SH NAME
palinear \- Perform Genome-Wide Association Analysis using a linear model
.SH SYNOPSIS
Modified: branches/ProbABEL-0.50/doc/palogist.1
===================================================================
--- branches/ProbABEL-0.50/doc/palogist.1 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/doc/palogist.1 2014-02-10 22:29:48 UTC (rev 1604)
@@ -1,4 +1,4 @@
-.TH palogist 1 "2 January 2014" "ProbABEL 0.4.2"
+.TH palogist 1 "2 January 2014" "ProbABEL 0.4.3"
.SH NAME
palogist \- Perform Genome-Wide Association Analysis using a linear model
.SH SYNOPSIS
Modified: branches/ProbABEL-0.50/doc/probabel.1
===================================================================
--- branches/ProbABEL-0.50/doc/probabel.1 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/doc/probabel.1 2014-02-10 22:29:48 UTC (rev 1604)
@@ -1,4 +1,4 @@
-.TH ProbABEL 1 "2 January 2014" "ProbABEL 0.4.2"
+.TH ProbABEL 1 "2 January 2014" "ProbABEL 0.4.3"
.SH NAME
probabel \- Wrapper around the three ProbABEL binaries, simplifying their use
.SH SYNOPSIS
Modified: branches/ProbABEL-0.50/src/command_line_settings.cpp
===================================================================
--- branches/ProbABEL-0.50/src/command_line_settings.cpp 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/src/command_line_settings.cpp 2014-02-10 22:29:48 UTC (rev 1604)
@@ -3,8 +3,29 @@
*
* Created on: Apr 1, 2012
* Author: mkooyman
+*
+ *
+ * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * the SVN commit logs for more details.
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ *
*/
+
#include <getopt.h>
#include <string>
#include <iostream>
Modified: branches/ProbABEL-0.50/src/command_line_settings.h
===================================================================
--- branches/ProbABEL-0.50/src/command_line_settings.h 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/src/command_line_settings.h 2014-02-10 22:29:48 UTC (rev 1604)
@@ -3,8 +3,29 @@
*
* Created on: Apr 2; int 2012
* Author: mkooyman
+*
+ *
+ * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * the SVN commit logs for more details.
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ *
*/
+
#ifndef COMMAND_LINE_SETTINGS_H_
#define COMMAND_LINE_SETTINGS_H_
#include <string>
Modified: branches/ProbABEL-0.50/src/coxph_data.cpp
===================================================================
--- branches/ProbABEL-0.50/src/coxph_data.cpp 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/src/coxph_data.cpp 2014-02-10 22:29:48 UTC (rev 1604)
@@ -3,7 +3,29 @@
*
* Created on: Mar 31, 2012
* Author: mkooyman
+ *
+ *
+ * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * the SVN commit logs for more details.
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ *
*/
+
+
#include "coxph_data.h"
#include <iostream>
#include <cmath>
Modified: branches/ProbABEL-0.50/src/coxph_data.h
===================================================================
--- branches/ProbABEL-0.50/src/coxph_data.h 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/src/coxph_data.h 2014-02-10 22:29:48 UTC (rev 1604)
@@ -3,8 +3,29 @@
*
* Created on: Mar 31, 2012
* Author: mkooyman
+ *
+ *
+ * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * the SVN commit logs for more details.
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ *
*/
+
#ifndef COXPH_DATA_H_
#define COXPH_DATA_H_
Modified: branches/ProbABEL-0.50/src/data.cpp
===================================================================
--- branches/ProbABEL-0.50/src/data.cpp 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/src/data.cpp 2014-02-10 22:29:48 UTC (rev 1604)
@@ -1,3 +1,26 @@
+/*
+ *
+ * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * the SVN commit logs for more details.
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ *
+ */
+
+
#include <string>
#include <sstream>
#include <fstream>
Modified: branches/ProbABEL-0.50/src/data.h
===================================================================
--- branches/ProbABEL-0.50/src/data.h 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/src/data.h 2014-02-10 22:29:48 UTC (rev 1604)
@@ -3,8 +3,29 @@
* \author mkooyman
*
* \brief Contains several classes we didn't put somewhere else yet
+ *
+ *
+ * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * the SVN commit logs for more details.
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ *
*/
+
#ifndef DATA_H_
#define DATA_H_
#include <string>
Modified: branches/ProbABEL-0.50/src/eigen_mematrix.cpp
===================================================================
--- branches/ProbABEL-0.50/src/eigen_mematrix.cpp 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/src/eigen_mematrix.cpp 2014-02-10 22:29:48 UTC (rev 1604)
@@ -1,3 +1,26 @@
+/*
+ *
+ * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * the SVN commit logs for more details.
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ *
+ */
+
+
#ifndef EIGEN_MEMATRI1_H
#define EIGEN_MEMATRI1_H
#include "eigen_mematrix.h"
Modified: branches/ProbABEL-0.50/src/eigen_mematrix.h
===================================================================
--- branches/ProbABEL-0.50/src/eigen_mematrix.h 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/src/eigen_mematrix.h 2014-02-10 22:29:48 UTC (rev 1604)
@@ -1,3 +1,26 @@
+/*
+ *
+ * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * the SVN commit logs for more details.
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ *
+ */
+
+
#ifndef __EIGEN_MEMATRIX_H__
#define __EIGEN_MEMATRIX_H__
#include <Eigen/Dense>
Modified: branches/ProbABEL-0.50/src/gendata.cpp
===================================================================
--- branches/ProbABEL-0.50/src/gendata.cpp 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/src/gendata.cpp 2014-02-10 22:29:48 UTC (rev 1604)
@@ -3,7 +3,29 @@
*
* Created on: Mar 8, 2012
* Author: mkooyman
+ *
+ *
+ * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * the SVN commit logs for more details.
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ *
*/
+
+
#include <string>
#include <errno.h>
#include "gendata.h"
Modified: branches/ProbABEL-0.50/src/gendata.h
===================================================================
--- branches/ProbABEL-0.50/src/gendata.h 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/src/gendata.h 2014-02-10 22:29:48 UTC (rev 1604)
@@ -3,8 +3,29 @@
*
* Created on: Mar 8, 2012
* Author: mkooyman
+ *
+ *
+ * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * the SVN commit logs for more details.
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ *
*/
+
#ifndef GENDATA_H_
#define GENDATA_H_
#include <string>
Modified: branches/ProbABEL-0.50/src/main.cpp
===================================================================
--- branches/ProbABEL-0.50/src/main.cpp 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/src/main.cpp 2014-02-10 22:29:48 UTC (rev 1604)
@@ -32,6 +32,30 @@
// Company: Department of Epidemiology, ErasmusMC Rotterdam, The Netherlands.
//
//=============================================================================
+
+/*
+ *
+ * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * the SVN commit logs for more details.
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ *
+ */
+
+
#include <stdio.h>
#include <iostream>
#include <cstdlib>
Modified: branches/ProbABEL-0.50/src/main_functions_dump.cpp
===================================================================
--- branches/ProbABEL-0.50/src/main_functions_dump.cpp 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/src/main_functions_dump.cpp 2014-02-10 22:29:48 UTC (rev 1604)
@@ -3,6 +3,26 @@
*
* Created on: Nov 27, 2013
* Author: mkooyman
+*
+ *
+ * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * the SVN commit logs for more details.
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ *
*/
Modified: branches/ProbABEL-0.50/src/main_functions_dump.h
===================================================================
--- branches/ProbABEL-0.50/src/main_functions_dump.h 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/src/main_functions_dump.h 2014-02-10 22:29:48 UTC (rev 1604)
@@ -3,8 +3,29 @@
*
* Created on: Nov 27, 2013
* Author: mkooyman
+ *
+ *
+ * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * the SVN commit logs for more details.
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ *
*/
+
#ifndef MAIN_FUNCTIONS_DUMP_H_
#define MAIN_FUNCTIONS_DUMP_H_
Modified: branches/ProbABEL-0.50/src/maskedmatrix.cpp
===================================================================
--- branches/ProbABEL-0.50/src/maskedmatrix.cpp 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/src/maskedmatrix.cpp 2014-02-10 22:29:48 UTC (rev 1604)
@@ -3,8 +3,29 @@
*
* Created on: May 22, 2012
* Author: mkooyman
+ *
+ *
+ * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * the SVN commit logs for more details.
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ *
*/
+
#include "maskedmatrix.h"
#if EIGEN
#include "eigen_mematrix.h"
Modified: branches/ProbABEL-0.50/src/maskedmatrix.h
===================================================================
--- branches/ProbABEL-0.50/src/maskedmatrix.h 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/src/maskedmatrix.h 2014-02-10 22:29:48 UTC (rev 1604)
@@ -3,8 +3,29 @@
*
* Created on: May 22, 2012
* Author: mkooyman
+ *
+ *
+ * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * the SVN commit logs for more details.
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ *
*/
+
#ifndef MASKEDMATRIX_H_
#define MASKEDMATRIX_H_
Modified: branches/ProbABEL-0.50/src/mematri1.h
===================================================================
--- branches/ProbABEL-0.50/src/mematri1.h 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/src/mematri1.h 2014-02-10 22:29:48 UTC (rev 1604)
@@ -1,3 +1,26 @@
+/*
+ *
+ * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * the SVN commit logs for more details.
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ *
+ */
+
+
#ifndef MEMATRI1_H
#define MEMATRI1_H
Modified: branches/ProbABEL-0.50/src/mematrix.h
===================================================================
--- branches/ProbABEL-0.50/src/mematrix.h 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/src/mematrix.h 2014-02-10 22:29:48 UTC (rev 1604)
@@ -1,3 +1,26 @@
+/*
+ *
+ * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * the SVN commit logs for more details.
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ *
+ */
+
+
#ifndef __MEMATRIX_H__
#define __MEMATRIX_H__
#include <iostream>
Modified: branches/ProbABEL-0.50/src/phedata.cpp
===================================================================
--- branches/ProbABEL-0.50/src/phedata.cpp 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/src/phedata.cpp 2014-02-10 22:29:48 UTC (rev 1604)
@@ -1,3 +1,26 @@
+/*
+ *
+ * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * the SVN commit logs for more details.
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ *
+ */
+
+
#include <phedata.h>
#include <string>
#include <sstream>
Modified: branches/ProbABEL-0.50/src/phedata.h
===================================================================
--- branches/ProbABEL-0.50/src/phedata.h 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/src/phedata.h 2014-02-10 22:29:48 UTC (rev 1604)
@@ -3,8 +3,29 @@
*
* Created on: Mar 6, 2012
* Author: mkooyman
+ *
+ *
+ * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * the SVN commit logs for more details.
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ *
*/
+
#ifndef PHEDATA_H_
#define PHEDATA_H_
Modified: branches/ProbABEL-0.50/src/reg1.cpp
===================================================================
--- branches/ProbABEL-0.50/src/reg1.cpp 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/src/reg1.cpp 2014-02-10 22:29:48 UTC (rev 1604)
@@ -1,3 +1,26 @@
+/*
+ *
+ * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * the SVN commit logs for more details.
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ *
+ */
+
+
#include "reg1.h"
mematrix<double> apply_model(mematrix<double>& X, int model, int interaction,
Modified: branches/ProbABEL-0.50/src/reg1.h
===================================================================
--- branches/ProbABEL-0.50/src/reg1.h 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/src/reg1.h 2014-02-10 22:29:48 UTC (rev 1604)
@@ -22,6 +22,30 @@
// Email: i.aoultchenko at erasmusmc.nl, m.struchalin at erasmusmc.nl
//
//==============================================================================
+
+/*
+ *
+ * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * the SVN commit logs for more details.
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ *
+ */
+
+
//#include "coxph_data.h"
#ifndef REG1_H_
#define REG1_H_
Modified: branches/ProbABEL-0.50/src/regdata.cpp
===================================================================
--- branches/ProbABEL-0.50/src/regdata.cpp 2014-02-09 21:36:36 UTC (rev 1603)
+++ branches/ProbABEL-0.50/src/regdata.cpp 2014-02-10 22:29:48 UTC (rev 1604)
@@ -3,8 +3,29 @@
*
* Created on: Mar 29, 2012
* Author: mkooyman
+ *
+ *
+ * Copyright (C) 2009--2014 Various members of the GenABEL team. See
+ * the SVN commit logs for more details.
+ *
+ * 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 2
+ * 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, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301, USA.
+ *
*/
+
#include "fvlib/AbstractMatrix.h"
#include "fvlib/CastUtils.h"
#include "fvlib/const.h"
@@ -14,6 +35,7 @@
#include "fvlib/frversion.h"
#include "fvlib/Logger.h"
#include "fvlib/Transposer.h"
+
#include <algorithm> // STL algoritms
#include "regdata.h"
@@ -40,7 +62,9 @@
freq = obj.freq;
is_interaction_excluded = obj.is_interaction_excluded;
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/genabel -r 1604
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