[med-svn] [probabel] 01/01: Imported Upstream version 0.4.3
Andreas Tille
tille at debian.org
Fri Apr 4 08:56:33 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch upstream
in repository probabel.
commit 80a055f5ba117944d40f6af4390fbdb52b466e33
Author: Andreas Tille <tille at debian.org>
Date: Fri Apr 4 10:32:30 2014 +0200
Imported Upstream version 0.4.3
---
checks/R-tests/Makefile.am | 5 +
checks/R-tests/Makefile.in | 3 +-
checks/R-tests/run_models_in_R_pacox.R | 5 +-
checks/run_diff.sh | 2 +-
configure | 20 +-
configure.ac | 4 +-
doc/ChangeLog | 12 +-
doc/INSTALL | 3 +
doc/Makefile.in | 4 +-
doc/ProbABEL_manual.tex | 225 ++++++-
doc/pacoxph.1 | 2 +-
doc/palinear.1 | 2 +-
doc/palogist.1 | 2 +-
doc/probabel.1 | 2 +-
doc/probabel.pl.1 | 2 +-
src/Makefile.in | 1005 +++++++++++++++-----------------
src/command_line_settings.cpp | 21 +
src/command_line_settings.h | 21 +
src/coxph_data.cpp | 22 +
src/coxph_data.h | 21 +
src/data.cpp | 23 +
src/data.h | 21 +
src/eigen_mematrix.cpp | 32 +-
src/eigen_mematrix.h | 23 +
src/gendata.cpp | 39 +-
src/gendata.h | 21 +
src/main.cpp | 24 +
src/main_functions_dump.cpp | 20 +
src/main_functions_dump.h | 21 +
src/maskedmatrix.cpp | 21 +
src/maskedmatrix.h | 21 +
src/mematri1.h | 23 +
src/mematrix.h | 23 +
src/phedata.cpp | 23 +
src/phedata.h | 21 +
src/reg1.cpp | 34 +-
src/reg1.h | 24 +
src/regdata.cpp | 22 +
src/regdata.h | 21 +
src/usage.cpp | 27 +-
src/usage.h | 21 +
src/utilities.cpp | 22 +
src/utilities.h | 21 +
43 files changed, 1342 insertions(+), 589 deletions(-)
diff --git a/checks/R-tests/Makefile.am b/checks/R-tests/Makefile.am
index 91332df..a88ce6c 100644
--- a/checks/R-tests/Makefile.am
+++ b/checks/R-tests/Makefile.am
@@ -30,6 +30,11 @@ TESTS = $(check_SCRIPTS)
## The palogist R test still doesn't run correctly.
XFAIL_TESTS = run_R_test_palogist.sh
+## The pacoxph R test fails on SNP 6 when EIGEN is not enabled.
+if !WITH_EIGEN
+XFAIL_TESTS += run_R_test_pacox.sh
+endif
+
EXTRA_DIST = $(check_SCRIPTS) $(R_test_files)
diff --git a/checks/R-tests/Makefile.in b/checks/R-tests/Makefile.in
index 17e4000..df0a3ec 100644
--- a/checks/R-tests/Makefile.in
+++ b/checks/R-tests/Makefile.in
@@ -78,6 +78,7 @@ POST_UNINSTALL = :
@BUILD_palinear_TRUE@@HAVE_R_TRUE at am__append_1 = run_R_test_palinear.sh
@BUILD_palogist_TRUE@@HAVE_R_TRUE at am__append_2 = run_R_test_palogist.sh
@BUILD_pacoxph_TRUE@@HAVE_R_TRUE at am__append_3 = run_R_test_pacox.sh
+ at WITH_EIGEN_FALSE@am__append_4 = run_R_test_pacox.sh
subdir = checks/R-tests
DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
$(top_srcdir)/test-driver
@@ -423,7 +424,7 @@ AM_TESTS_ENVIRONMENT = \
PA_BINDIR=$(top_builddir)/src
TESTS = $(check_SCRIPTS)
-XFAIL_TESTS = run_R_test_palogist.sh
+XFAIL_TESTS = run_R_test_palogist.sh $(am__append_4)
EXTRA_DIST = $(check_SCRIPTS) $(R_test_files)
##################################################
diff --git a/checks/R-tests/run_models_in_R_pacox.R b/checks/R-tests/run_models_in_R_pacox.R
index d1cfa0e..992f6c5 100644
--- a/checks/R-tests/run_models_in_R_pacox.R
+++ b/checks/R-tests/run_models_in_R_pacox.R
@@ -1,5 +1,8 @@
cat("Checking Cox PH regression...\n")
-library(survival)
+if (!require(survival)) {
+ cat("The R package 'survival' is not installed. Skipping Cox PH checks\n")
+ q()
+}
args <- commandArgs(TRUE)
srcdir <- args[1]
diff --git a/checks/run_diff.sh b/checks/run_diff.sh
index 7c9a44e..132e2b1 100644
--- a/checks/run_diff.sh
+++ b/checks/run_diff.sh
@@ -20,7 +20,7 @@ run_diff()
blanks=" "
- if diff "$file1" "$file2" $args; then
+ if diff $args "$file1" "$file2"; then
echo -e "${name}${blanks:${#name}} OK"
else
echo -e "${name}${blanks:${#name}} FAILED"
diff --git a/configure b/configure
index 22b3659..bb7b684 100755
--- a/configure
+++ b/configure
@@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for ProbABEL 0.4.2.
+# Generated by GNU Autoconf 2.69 for ProbABEL 0.4.3.
#
# Report bugs to <genabel-devel at r-forge.wu-wien.ac.at>.
#
@@ -580,8 +580,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='ProbABEL'
PACKAGE_TARNAME='probabel'
-PACKAGE_VERSION='0.4.2'
-PACKAGE_STRING='ProbABEL 0.4.2'
+PACKAGE_VERSION='0.4.3'
+PACKAGE_STRING='ProbABEL 0.4.3'
PACKAGE_BUGREPORT='genabel-devel at r-forge.wu-wien.ac.at'
PACKAGE_URL=''
@@ -1305,7 +1305,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures ProbABEL 0.4.2 to adapt to many kinds of systems.
+\`configure' configures ProbABEL 0.4.3 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1371,7 +1371,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of ProbABEL 0.4.2:";;
+ short | recursive ) echo "Configuration of ProbABEL 0.4.3:";;
esac
cat <<\_ACEOF
@@ -1484,7 +1484,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-ProbABEL configure 0.4.2
+ProbABEL configure 0.4.3
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1945,7 +1945,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
-It was created by ProbABEL $as_me 0.4.2, which was
+It was created by ProbABEL $as_me 0.4.3, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@@ -2808,7 +2808,7 @@ fi
# Define the identity of the package.
PACKAGE='probabel'
- VERSION='0.4.2'
+ VERSION='0.4.3'
cat >>confdefs.h <<_ACEOF
@@ -6491,7 +6491,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by ProbABEL $as_me 0.4.2, which was
+This file was extended by ProbABEL $as_me 0.4.3, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -6557,7 +6557,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-ProbABEL config.status 0.4.2
+ProbABEL config.status 0.4.3
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
diff --git a/configure.ac b/configure.ac
index d78aa76..3a59486 100644
--- a/configure.ac
+++ b/configure.ac
@@ -2,8 +2,8 @@
# 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)
-AM_INIT_AUTOMAKE([silent-rules])
+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])
AC_CONFIG_HEADERS([src/config.h])
diff --git a/doc/ChangeLog b/doc/ChangeLog
index 848c466..22ff7ed 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,13 @@
-***** v.0.4.2
+***** v.0.4.3 (2014.04.01)
+* Speed-up of a factor of ~ 2 for linear, logistic and Cox regression when
+ using filevector input files.
+* Fixed bug #5404: "ProbABEL's R check for Cox regression doesn't check if
+ the survival package is installed".
+* Fixed bug #5403: "The ProbABEL manual doesn't contain any information on
+ how to install ProbABEL"
+
+
+***** v.0.4.2 (2014.01.02)
* The 'probabel.pl' script is now simply renamed to 'probabel' (a user
shouldn't care what scripting language we use). For at least several
releases to come, the old script name will still exist (as a link to the
@@ -26,6 +35,7 @@
* For developers: a start has been made on documenting the internal
functions using Doxygen.
+
***** v.0.4.1 (2013.08.29)
* Fix bug #4854: When using mmscore, there is one (nan) column missing in
the output for low-frequency SNPs. Also includes a simplification of the
diff --git a/doc/INSTALL b/doc/INSTALL
index edf7340..700a113 100644
--- a/doc/INSTALL
+++ b/doc/INSTALL
@@ -1,5 +1,8 @@
These instructions show how to build ProbABEL.
+The ProbABEL manual (in .tex or .pdf format) also contains detailed
+(complementary) instructions on how to obtain and install ProbABEL.
+
* Dependencies
ProbABEL can be compiled without depending on other
libraries. However, when the Eigen library is present
diff --git a/doc/Makefile.in b/doc/Makefile.in
index e0f999e..b93b8c0 100644
--- a/doc/Makefile.in
+++ b/doc/Makefile.in
@@ -283,9 +283,9 @@ $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am $(am__confi
exit 1;; \
esac; \
done; \
- echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign doc/Makefile'; \
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu doc/Makefile'; \
$(am__cd) $(top_srcdir) && \
- $(AUTOMAKE) --foreign doc/Makefile
+ $(AUTOMAKE) --gnu doc/Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
diff --git a/doc/ProbABEL_manual.tex b/doc/ProbABEL_manual.tex
index e20e7d0..aeba9cd 100644
--- a/doc/ProbABEL_manual.tex
+++ b/doc/ProbABEL_manual.tex
@@ -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$^{1,3}$ \\
@@ -11,13 +11,46 @@
$^{2}${\small Erasmus MC, Rotterdam}\\
$^{3}${\small Institute of Cytology and Genetics SD RAS, Novosibirsk}
}
-\date{January 2, 2014}
+\date{April 1, 2014}
+
+
+\usepackage[utf8]{inputenc}
+\usepackage[T1]{fontenc}
+\usepackage{textcomp}
+
+\usepackage[svgnames]{xcolor}
+\definecolor{webgreen}{rgb}{0,.5,0}
\usepackage{verbatim}
+
+\usepackage{listings}
+\lstloadlanguages{Bash}
+\definecolor{lstbgcolor}{rgb}{0.9,0.9,0.9}
+\lstset{
+ tabsize=4,
+ rulecolor=,
+ basicstyle=\ttfamily,
+ upquote=true,
+ columns=fixed,
+ showstringspaces=false,
+ extendedchars=true,
+ breaklines=true,
+ breakatwhitespace,
+ prebreak = \raisebox{0ex}[0ex][0ex]{\ensuremath{\hookleftarrow}},
+ frame=single,
+ showtabs=false,
+ showspaces=false,
+ showstringspaces=false,
+ keywordstyle=\color[rgb]{0,0,1},
+ commentstyle=\color[rgb]{0,0.4,0},
+ stringstyle=\color[rgb]{0.5,0,1},
+ basicstyle=\footnotesize\ttfamily,
+ backgroundcolor=\color{lstbgcolor},
+}
+
\usepackage{titleref}
\usepackage{amsmath}
\usepackage{makeidx}
-\usepackage[dvipsnames]{xcolor}
\usepackage[pdftex,hyperfootnotes=false,pdfpagelabels]{hyperref}
\hypersetup{%
linktocpage=false, % If true the page numbers in the toc are links
@@ -29,7 +62,7 @@
pdfhighlight=/O, %hyperfootnotes=true,%nesting=true,%frenchlinks,%
pdfauthor={\textcopyright\ Y.~Aulchenko, M.~Struchalin, L.C.~Karssen},
pdfsubject={ProbABEL manual},
- colorlinks=true, urlcolor=MidnightBlue, linkcolor=blue %
+ colorlinks=true, urlcolor=blue, linkcolor=blue, citecolor=webgreen %
}
% get the links to the figures and tables right:
\usepackage[all]{hypcap} % to be loaded after hyperref package
@@ -109,6 +142,141 @@ questions, please turn to our forum at
GenABEL project bug tracker at
\url{https://r-forge.r-project.org/tracker/index.php?group_id=505&atid=2058}.
+\section{Obtaining and installing \PA}
+\label{sec:obtaininstall}
+\PA{} is a tool that is mostly used on computers running the Linux
+operating system. We try to publish binary packages for Windows as
+well, but these aren't tested. We strongly suggest using \PA{} on
+Linux.
+
+\subsection{Precompiled packages}
+\PA{} can be obtained in several ways:
+\begin{itemize}
+\item If you are using Ubuntu Linux and have administrative rights on
+ the machine you can add the GenABEL PPA to your APT configuration
+ and install it from there. The PPA can be found at
+ \url{https://launchpad.net/~l.c.karssen/+archive/genabel-ppa}. Instructions
+ on how to add the PPA can also be found there.
+\item If your computer runs Debian Linux\footnote{At the moment \PA{}
+ is only available in Debian testing and unstable.} (and you have
+ administrative rights on it), you can install ProbABEL like this:
+ \begin{lstlisting}
+user at server:~$ apt-get install probabel
+ \end{lstlisting}
+\item Zip files with pre-compiled binaries (if available) can be found
+ on the ProbABEL web page
+ (\url{http://www.genabel.org/packages/ProbABEL}).
+\item If you don't fall in any of the aforementioned
+ categories\footnote{We know that many people have use Red Hat Linux,
+ CentOS, Scientific Linux or any other Red Hat
+ derivative. Unfortunately we haven't got \texttt{rpm} files
+ yet. Any help in creating those will be highly appreciated}, you
+ can install \PA{} manually by downloading the source code of the
+ latest version from the website and compiling it yourself. This will
+ be explained in section~\ref{sec:obtain}.
+\end{itemize}
+
+
+\subsection{Obtaining the source code and compiling it yourself}
+\label{sec:obtain}
+If you can't use any of the aforementioned pre-compiled packages, you
+can download the source code of \PA{} yourself, compile it and run it
+from your own home directory. This section details the steps you need
+to take. More information can be found in the \texttt{doc/INSTALL}.
+
+On the \href{http://www.genabel.org/packages/probabel}{\PA{}} website
+you can find the link to the latest version of the source code of \PA{}
+in a \texttt{tar.gz} file\footnote{The \texttt{tar.gz} file archive
+ format is the most commonly used format for distributing source code
+ on Linux/UNIX systems. These are compressed files, similar to
+ \texttt{zip} files.}. A \texttt{.asc} file with the same base name
+as the source code archive is also provided. This file contains a
+so-called GPG signature of the \texttt{tar.gz} file. Using this file
+and the \texttt{gpg} tool you can verify the authenticity of the
+source code by typing this command on the command line of a Linux
+shell\footnote{The \$ sign indicates the end of the command line
+ prompt. You don't need to type it.}:
+\begin{lstlisting}[]
+user at server:~$ gpg --verify probabel-0.4.3.tar.gz.asc
+gpg: Signature made Thu Jan 2 02:38:25 2014 CET using DSA key ID DA9CD509
+gpg: Good signature from "L.C. Karssen (GPG key for personal stuff) <lennart at karssen.org>"
+gpg: aka "L.C. Karssen (My GMail address) <l.c.karssen at gmail.com>"
+\end{lstlisting}
+Notice the ``Good signature'' message and the fact that the package was
+signed by Lennart Karssen, the ProbABEL maintainer. If a malicious
+hacker would have replaced the source code file (for example with one
+including a virus), he won't be able to sign the package using the
+same key (with key ID DA9CD509). If, for some reason, the
+\texttt{tar.gz} file has changed (e.g.~by such a hacker or because
+the file didn't get downloaded correctly) you will see output like
+this (notice the ``BAD signature'' message):
+\begin{lstlisting}[]
+user at server:~$ gpg --verify probabel-0.4.2.tar.gz.asc
+gpg: Signature made Thu Jan 2 02:38:25 2014 CET using DSA key ID DA9CD509
+gpg: BAD signature from "L.C. Karssen (GPG key for personal stuff) <lennart at karssen.org>"
+user at server:~$
+\end{lstlisting}
+
+Before continuing, it is important to mention that \PA{} can make use
+of the EIGEN library\footnote{EIGEN is a library for fast matrix
+ multiplication.}. We strongly recommend compiling \PA with EIGEN as
+it will speed up your analyses considerably. Moreover, we plan to
+remove the non-EIGEN part of the code in a future release. So, go to
+\url{http://eigen.tuxfamily.org} and download the \texttt{tar.gz} file
+of the latest version of EIGEN (3.2.1 at the time of writing). Extract
+the files:
+\begin{lstlisting}
+user at server:~$ tar -xzf 3.2.1.tar.gz
+\end{lstlisting}
+This will create a directory called \texttt{eigen-eigen} followed by a
+series of letters and digits. For simplicity we rename it to EIGEN
+\begin{lstlisting}
+user at server:~$ mv eigen-eigen-6b38706d90a9 EIGEN
+\end{lstlisting}
+
+Now it's time to extract the \PA{} source code and move into the
+directory that is created:
+\begin{lstlisting}
+user at server:~$ tar -xzf probabel-0.4.3.tar.gz
+user at server:~$ cd probabel-0.4.3
+\end{lstlisting}
+With the following command we will indicate where the EIGEN files can
+be found and where we want to install \PA{}. Let's install in a
+subdirectory of your home directory,
+e.g.~\texttt{/home/yourusername/ProbABEL}:
+\begin{lstlisting}
+user at server:~$ ./configure \
+ --prefix=/home/yourusername/ProbABEL/ \
+ --with-eigen-include-path=/home/yourusername/EIGEN
+\end{lstlisting}
+This will be followed by a series of checks to see if all tools
+required for compilation and installation are present on your
+system. If you don't see any warnings you can continue to
+compile\footnote{Compilation is the process of converting the source
+ files containing human readable program code to a files with machine
+ readable instructions.} the code using the \texttt{make}
+command\footnote{If you work on a machine with multiple processors (or
+ processor cores), which should be the case on modern servers, but
+ also on most PCs, you can speed up the process by adding this number
+ to the \texttt{-j} option. For example for four cores run
+ \texttt{make -j4}.} The next step will check the compiled code,
+after wich you install the program, documentation and examples to the
+directory you specified previously with the \texttt{--prefix} argument
+to the \texttt{./configure} command.
+\begin{lstlisting}
+user at server:~$ make
+user at server:~$ make check
+user at server:~$ make install
+\end{lstlisting}
+Note that each of these steps will scroll a lot of output on the
+screen. Please watch it for any warnings or errors. Please ask any
+questions on \href{http://forum.genabel.org/}{our support forum}.
+
+If all went well you will find the executable programs
+(\texttt{palinear}, \texttt{palogist}, and \texttt{pacoxph}) in the
+directory \texttt{/home/yourusername/ProbABEL/bin/}. You are now ready
+to analyse your data!
+
\section{Input files}
\PA{} takes three files as input: a file containing SNP
information (e.g.~the MLINFO file of MaCH), a file with genome- or
@@ -295,7 +463,7 @@ you run either program with the \texttt{--help} option, you will get a
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
@@ -337,33 +505,29 @@ user at server$ man palinear
However, for a simple run only three options are mandatory, which
specify the necessary files needed to run the regression analysis.
-These options are
-\texttt{--dose} (or \texttt{-d}),
-specifying the genomic predictor/MLDOSE file described in section \ref{ssec:dosein};
-\texttt{--pheno} (or \texttt{-p}),
-specifying the phenotypic data file described in section \ref{ssec:phenoin}; and
-\texttt{--info} (or \texttt{-i}),
-specifying the SNP information file described in section \ref{ssec:infoin}.
+These options are \texttt{--dose} (or \texttt{-d}), specifying the
+genomic predictor/MLDOSE file described in section \ref{ssec:dosein};
+\texttt{--pheno} (or \texttt{-p}), specifying the phenotypic data file
+described in section \ref{ssec:phenoin}; and \texttt{--info} (or
+\texttt{-i}), specifying the SNP information file described in section
+\ref{ssec:infoin}.
If you change to the \texttt{examples} directory you can run
an analysis of height by running
\begin{verbatim}
-user at server:~/ProbABEL/examples/$ ../bin/palinear -p height.txt \
- -d test.mldose -i test.mlinfo
+palinear -p height.txt -d gtdata/test.mldose -i gtdata/test.mlinfo
\end{verbatim}
-Output from the analysis will be directed to the
+Output from the analysis will be stored in the
\texttt{regression.out.csv} file.
-
The analysis of a binary trait (e.g.~chd) can be run with
\begin{verbatim}
-user at server:~/ProbABEL/examples/$ ../bin/palogist -p logist_data.txt \
- -d test.mldose -i test.mlinfo
+palogist -p logist_data.txt -d gtdata/test.mldose \
+ -i gtdata/test.mlinfo
\end{verbatim}
-
To run a Cox proportional hazards model, try
\begin{verbatim}
-user at server:~/ProbABEL/examples/$ ../bin/pacoxph -p coxph_data.txt \
- -d test.mldose -i test.mlinfo
+pacoxph -p coxph_data.txt -d gtdata/test.mldose \
+ -i gtdata/test.mlinfo
\end{verbatim}
Please have a look at the shell script files \texttt{example\_qt.sh},
@@ -372,11 +536,20 @@ a better overview of the analysis options.
To run an analysis with MLPROB files, you need specify the MLPROB file
with the \texttt{-d} option and also specify that there are two
-genetic predictors per SNP, e.g.~you can run linear model with
+genetic predictors per SNP, e.g.~you can run a linear model with
+\begin{verbatim}
+palinear -p height.txt -d gtdata/test.mlprob -i gtdata/test.mlinfo \
+ --ngpreds=2
+\end{verbatim}
+
+When using genomic predictor files (dosages or probabilities) stored
+in filevector (a.k.a.~DatABEL) format (i.e.~a combination of
+\texttt{.fvi} and \texttt{.fvd} files) you can specify these like you
+would with ordinary text files. This is how the previous example would
+change:
\begin{verbatim}
-user at server:~/ProbABEL/examples/$ ../bin/palinear -p height.txt \
- -d test.mlprob -i test.mlinfo \
- --ngpreds=2
+palinear -p height.txt -d gtdata/test.mlprob.fvi -i gtdata/test.mlinfo \
+ --ngpreds=2
\end{verbatim}
\subsection{Advanced analysis options}
@@ -855,7 +1028,7 @@ BMC Bioinformatics. 2010, 11:134.
\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}
diff --git a/doc/pacoxph.1 b/doc/pacoxph.1
index 2359961..4fe3121 100644
--- a/doc/pacoxph.1
+++ b/doc/pacoxph.1
@@ -1,4 +1,4 @@
-.TH pacoxph 1 "2 January 2014" "ProbABEL 0.4.2"
+.TH pacoxph 1 "01 April 2014" "ProbABEL 0.4.3"
.SH NAME
pacoxph \- Perform Genome-Wide Association Analysis using a linear model
.SH SYNOPSIS
diff --git a/doc/palinear.1 b/doc/palinear.1
index 95743ca..ecdf295 100644
--- a/doc/palinear.1
+++ b/doc/palinear.1
@@ -1,4 +1,4 @@
-.TH palinear 1 "2 January 2014" "ProbABEL 0.4.2"
+.TH palinear 1 "01 April 2014" "ProbABEL 0.4.3"
.SH NAME
palinear \- Perform Genome-Wide Association Analysis using a linear model
.SH SYNOPSIS
diff --git a/doc/palogist.1 b/doc/palogist.1
index 7cbf8ec..e950026 100644
--- a/doc/palogist.1
+++ b/doc/palogist.1
@@ -1,4 +1,4 @@
-.TH palogist 1 "2 January 2014" "ProbABEL 0.4.2"
+.TH palogist 1 "01 April 2014" "ProbABEL 0.4.3"
.SH NAME
palogist \- Perform Genome-Wide Association Analysis using a linear model
.SH SYNOPSIS
diff --git a/doc/probabel.1 b/doc/probabel.1
index d818345..bd37640 100644
--- a/doc/probabel.1
+++ b/doc/probabel.1
@@ -1,4 +1,4 @@
-.TH ProbABEL 1 "2 January 2014" "ProbABEL 0.4.2"
+.TH ProbABEL 1 "01 April 2014" "ProbABEL 0.4.3"
.SH NAME
probabel \- Wrapper around the three ProbABEL binaries, simplifying their use
.SH SYNOPSIS
diff --git a/doc/probabel.pl.1 b/doc/probabel.pl.1
index d818345..bd37640 100644
--- a/doc/probabel.pl.1
+++ b/doc/probabel.pl.1
@@ -1,4 +1,4 @@
-.TH ProbABEL 1 "2 January 2014" "ProbABEL 0.4.2"
+.TH ProbABEL 1 "01 April 2014" "ProbABEL 0.4.3"
.SH NAME
probabel \- Wrapper around the three ProbABEL binaries, simplifying their use
.SH SYNOPSIS
diff --git a/src/Makefile.in b/src/Makefile.in
index c649499..7093c49 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -109,11 +109,13 @@ CONFIG_CLEAN_VPATH_FILES =
am__installdirs = "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)" \
"$(DESTDIR)$(scriptdir)" "$(DESTDIR)$(sysconfdir)"
PROGRAMS = $(bin_PROGRAMS)
-am__objects_1 = AbstractMatrix.$(OBJEXT) CastUtils.$(OBJEXT) \
- convert_util.$(OBJEXT) FileVector.$(OBJEXT) \
- FilteredMatrix.$(OBJEXT) frutil.$(OBJEXT) Logger.$(OBJEXT) \
- RealHandlerWrapper.$(OBJEXT) ReusableFileHandle.$(OBJEXT) \
- Transposer.$(OBJEXT)
+am__dirstamp = $(am__leading_dot)dirstamp
+am__objects_1 = fvlib/AbstractMatrix.$(OBJEXT) \
+ fvlib/CastUtils.$(OBJEXT) fvlib/convert_util.$(OBJEXT) \
+ fvlib/FileVector.$(OBJEXT) fvlib/FilteredMatrix.$(OBJEXT) \
+ fvlib/frutil.$(OBJEXT) fvlib/Logger.$(OBJEXT) \
+ fvlib/RealHandlerWrapper.$(OBJEXT) \
+ fvlib/ReusableFileHandle.$(OBJEXT) fvlib/Transposer.$(OBJEXT)
am__objects_2 =
am_extract_snp_OBJECTS = extract-snp.$(OBJEXT) $(am__objects_1) \
$(am__objects_2)
@@ -156,13 +158,15 @@ am__objects_5 = pacoxph-data.$(OBJEXT) pacoxph-gendata.$(OBJEXT) \
pacoxph-cholesky.$(OBJEXT) pacoxph-regdata.$(OBJEXT) \
pacoxph-maskedmatrix.$(OBJEXT) pacoxph-reg1.$(OBJEXT) \
pacoxph-main_functions_dump.$(OBJEXT)
-am__objects_6 = pacoxph-AbstractMatrix.$(OBJEXT) \
- pacoxph-CastUtils.$(OBJEXT) pacoxph-convert_util.$(OBJEXT) \
- pacoxph-FileVector.$(OBJEXT) pacoxph-FilteredMatrix.$(OBJEXT) \
- pacoxph-frutil.$(OBJEXT) pacoxph-Logger.$(OBJEXT) \
- pacoxph-RealHandlerWrapper.$(OBJEXT) \
- pacoxph-ReusableFileHandle.$(OBJEXT) \
- pacoxph-Transposer.$(OBJEXT)
+am__objects_6 = fvlib/pacoxph-AbstractMatrix.$(OBJEXT) \
+ fvlib/pacoxph-CastUtils.$(OBJEXT) \
+ fvlib/pacoxph-convert_util.$(OBJEXT) \
+ fvlib/pacoxph-FileVector.$(OBJEXT) \
+ fvlib/pacoxph-FilteredMatrix.$(OBJEXT) \
+ fvlib/pacoxph-frutil.$(OBJEXT) fvlib/pacoxph-Logger.$(OBJEXT) \
+ fvlib/pacoxph-RealHandlerWrapper.$(OBJEXT) \
+ fvlib/pacoxph-ReusableFileHandle.$(OBJEXT) \
+ fvlib/pacoxph-Transposer.$(OBJEXT)
am__objects_7 = pacoxph-eigen_mematrix.$(OBJEXT)
@WITH_EIGEN_TRUE at am__objects_8 = $(am__objects_7)
am_pacoxph_OBJECTS = $(am__objects_4) $(am__objects_5) \
@@ -195,14 +199,16 @@ am__objects_9 = palinear-data.$(OBJEXT) palinear-gendata.$(OBJEXT) \
palinear-cholesky.$(OBJEXT) palinear-regdata.$(OBJEXT) \
palinear-maskedmatrix.$(OBJEXT) palinear-reg1.$(OBJEXT) \
palinear-main_functions_dump.$(OBJEXT)
-am__objects_10 = palinear-AbstractMatrix.$(OBJEXT) \
- palinear-CastUtils.$(OBJEXT) palinear-convert_util.$(OBJEXT) \
- palinear-FileVector.$(OBJEXT) \
- palinear-FilteredMatrix.$(OBJEXT) palinear-frutil.$(OBJEXT) \
- palinear-Logger.$(OBJEXT) \
- palinear-RealHandlerWrapper.$(OBJEXT) \
- palinear-ReusableFileHandle.$(OBJEXT) \
- palinear-Transposer.$(OBJEXT)
+am__objects_10 = fvlib/palinear-AbstractMatrix.$(OBJEXT) \
+ fvlib/palinear-CastUtils.$(OBJEXT) \
+ fvlib/palinear-convert_util.$(OBJEXT) \
+ fvlib/palinear-FileVector.$(OBJEXT) \
+ fvlib/palinear-FilteredMatrix.$(OBJEXT) \
+ fvlib/palinear-frutil.$(OBJEXT) \
+ fvlib/palinear-Logger.$(OBJEXT) \
+ fvlib/palinear-RealHandlerWrapper.$(OBJEXT) \
+ fvlib/palinear-ReusableFileHandle.$(OBJEXT) \
+ fvlib/palinear-Transposer.$(OBJEXT)
am__objects_11 = palinear-eigen_mematrix.$(OBJEXT)
@WITH_EIGEN_TRUE at am__objects_12 = $(am__objects_11)
am_palinear_OBJECTS = $(am__objects_9) $(am__objects_10) \
@@ -234,14 +240,16 @@ am__objects_13 = palogist-data.$(OBJEXT) palogist-gendata.$(OBJEXT) \
palogist-cholesky.$(OBJEXT) palogist-regdata.$(OBJEXT) \
palogist-maskedmatrix.$(OBJEXT) palogist-reg1.$(OBJEXT) \
palogist-main_functions_dump.$(OBJEXT)
-am__objects_14 = palogist-AbstractMatrix.$(OBJEXT) \
- palogist-CastUtils.$(OBJEXT) palogist-convert_util.$(OBJEXT) \
- palogist-FileVector.$(OBJEXT) \
- palogist-FilteredMatrix.$(OBJEXT) palogist-frutil.$(OBJEXT) \
- palogist-Logger.$(OBJEXT) \
- palogist-RealHandlerWrapper.$(OBJEXT) \
- palogist-ReusableFileHandle.$(OBJEXT) \
- palogist-Transposer.$(OBJEXT)
+am__objects_14 = fvlib/palogist-AbstractMatrix.$(OBJEXT) \
+ fvlib/palogist-CastUtils.$(OBJEXT) \
+ fvlib/palogist-convert_util.$(OBJEXT) \
+ fvlib/palogist-FileVector.$(OBJEXT) \
+ fvlib/palogist-FilteredMatrix.$(OBJEXT) \
+ fvlib/palogist-frutil.$(OBJEXT) \
+ fvlib/palogist-Logger.$(OBJEXT) \
+ fvlib/palogist-RealHandlerWrapper.$(OBJEXT) \
+ fvlib/palogist-ReusableFileHandle.$(OBJEXT) \
+ fvlib/palogist-Transposer.$(OBJEXT)
am__objects_15 = palogist-eigen_mematrix.$(OBJEXT)
@WITH_EIGEN_TRUE at am__objects_16 = $(am__objects_15)
am_palogist_OBJECTS = $(am__objects_13) $(am__objects_14) \
@@ -510,9 +518,9 @@ $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am $(am__confi
exit 1;; \
esac; \
done; \
- echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign src/Makefile'; \
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/Makefile'; \
$(am__cd) $(top_srcdir) && \
- $(AUTOMAKE) --foreign src/Makefile
+ $(AUTOMAKE) --gnu src/Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
@case '$?' in \
@@ -588,18 +596,104 @@ uninstall-binPROGRAMS:
clean-binPROGRAMS:
-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+fvlib/$(am__dirstamp):
+ @$(MKDIR_P) fvlib
+ @: > fvlib/$(am__dirstamp)
+fvlib/$(DEPDIR)/$(am__dirstamp):
+ @$(MKDIR_P) fvlib/$(DEPDIR)
+ @: > fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/AbstractMatrix.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/CastUtils.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/convert_util.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/FileVector.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/FilteredMatrix.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/frutil.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/Logger.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/RealHandlerWrapper.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/ReusableFileHandle.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/Transposer.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
extract-snp$(EXEEXT): $(extract_snp_OBJECTS) $(extract_snp_DEPENDENCIES) $(EXTRA_extract_snp_DEPENDENCIES)
@rm -f extract-snp$(EXEEXT)
$(AM_V_CXXLD)$(CXXLINK) $(extract_snp_OBJECTS) $(extract_snp_LDADD) $(LIBS)
+fvlib/pacoxph-AbstractMatrix.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/pacoxph-CastUtils.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/pacoxph-convert_util.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/pacoxph-FileVector.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/pacoxph-FilteredMatrix.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/pacoxph-frutil.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/pacoxph-Logger.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/pacoxph-RealHandlerWrapper.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/pacoxph-ReusableFileHandle.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/pacoxph-Transposer.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
pacoxph$(EXEEXT): $(pacoxph_OBJECTS) $(pacoxph_DEPENDENCIES) $(EXTRA_pacoxph_DEPENDENCIES)
@rm -f pacoxph$(EXEEXT)
$(AM_V_CXXLD)$(pacoxph_LINK) $(pacoxph_OBJECTS) $(pacoxph_LDADD) $(LIBS)
+fvlib/palinear-AbstractMatrix.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/palinear-CastUtils.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/palinear-convert_util.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/palinear-FileVector.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/palinear-FilteredMatrix.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/palinear-frutil.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/palinear-Logger.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/palinear-RealHandlerWrapper.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/palinear-ReusableFileHandle.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/palinear-Transposer.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
palinear$(EXEEXT): $(palinear_OBJECTS) $(palinear_DEPENDENCIES) $(EXTRA_palinear_DEPENDENCIES)
@rm -f palinear$(EXEEXT)
$(AM_V_CXXLD)$(palinear_LINK) $(palinear_OBJECTS) $(palinear_LDADD) $(LIBS)
+fvlib/palogist-AbstractMatrix.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/palogist-CastUtils.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/palogist-convert_util.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/palogist-FileVector.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/palogist-FilteredMatrix.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/palogist-frutil.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/palogist-Logger.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/palogist-RealHandlerWrapper.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/palogist-ReusableFileHandle.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
+fvlib/palogist-Transposer.$(OBJEXT): fvlib/$(am__dirstamp) \
+ fvlib/$(DEPDIR)/$(am__dirstamp)
palogist$(EXEEXT): $(palogist_OBJECTS) $(palogist_DEPENDENCIES) $(EXTRA_palogist_DEPENDENCIES)
@rm -f palogist$(EXEEXT)
@@ -642,41 +736,22 @@ uninstall-dist_binSCRIPTS:
mostlyclean-compile:
-rm -f *.$(OBJEXT)
+ -rm -f fvlib/*.$(OBJEXT)
distclean-compile:
-rm -f *.tab.c
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/AbstractMatrix.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/CastUtils.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/FileVector.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/FilteredMatrix.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/Logger.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/RealHandlerWrapper.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/ReusableFileHandle.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/Transposer.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/convert_util.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/extract-snp.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/frutil.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-AbstractMatrix.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-CastUtils.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-FileVector.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-FilteredMatrix.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-Logger.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-RealHandlerWrapper.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-ReusableFileHandle.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-Transposer.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-chinv2.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-cholesky.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-cholesky2.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-chsolve2.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-command_line_settings.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-convert_util.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-coxfit2.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-coxph_data.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-data.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-dmatrix.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-eigen_mematrix.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-frutil.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-gendata.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-main.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-main_functions_dump.Po at am__quote@
@@ -686,20 +761,10 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-regdata.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-usage.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pacoxph-utilities.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-AbstractMatrix.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-CastUtils.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-FileVector.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-FilteredMatrix.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-Logger.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-RealHandlerWrapper.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-ReusableFileHandle.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-Transposer.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-cholesky.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-command_line_settings.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-convert_util.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-data.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-eigen_mematrix.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-frutil.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-gendata.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-main.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-main_functions_dump.Po at am__quote@
@@ -709,20 +774,10 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-regdata.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-usage.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palinear-utilities.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-AbstractMatrix.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-CastUtils.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-FileVector.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-FilteredMatrix.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-Logger.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-RealHandlerWrapper.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-ReusableFileHandle.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-Transposer.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-cholesky.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-command_line_settings.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-convert_util.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-data.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-eigen_mematrix.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-frutil.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-gendata.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-main.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/palogist-main_functions_dump.Po at am__quote@
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pacoxph-data.o: data.cpp
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@@ -1139,145 +1098,145 @@ pacoxph-main_functions_dump.obj: main_functions_dump.cpp
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+fvlib/pacoxph-AbstractMatrix.o: fvlib/AbstractMatrix.cpp
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pacoxph-coxph_data.o: coxph_data.cpp
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@@ -1475,145 +1434,145 @@ palinear-main_functions_dump.obj: main_functions_dump.cpp
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palinear-eigen_mematrix.o: eigen_mematrix.cpp
@am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palinear_CPPFLAGS) $(CPPFLAGS) $(palinear_CXXFLAGS) $(CXXFLAGS) -MT palinear-eigen_mematrix.o -MD -MP -MF $(DEPDIR)/palinear-eigen_mematrix.Tpo -c -o palinear-eigen_mematrix.o `test -f 'eigen_mematrix.cpp' || echo '$(srcdir)/'`eigen_mematrix.cpp
@@ -1797,145 +1756,145 @@ palogist-main_functions_dump.obj: main_functions_dump.cpp
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@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -c -o palogist-Transposer.o `test -f 'fvlib/Transposer.cpp' || echo '$(srcdir)/'`fvlib/Transposer.cpp
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -c -o fvlib/palogist-Transposer.o `test -f 'fvlib/Transposer.cpp' || echo '$(srcdir)/'`fvlib/Transposer.cpp
-palogist-Transposer.obj: fvlib/Transposer.cpp
- at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -MT palogist-Transposer.obj -MD -MP -MF $(DEPDIR)/palogist-Transposer.Tpo -c -o palogist-Transposer.obj `if test -f 'fvlib/Transposer.cpp'; then $(CYGPATH_W) 'fvlib/Transposer.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/Transposer.cpp'; fi`
- at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/palogist-Transposer.Tpo $(DEPDIR)/palogist-Transposer.Po
- at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='fvlib/Transposer.cpp' object='palogist-Transposer.obj' libtool=no @AMDEPBACKSLASH@
+fvlib/palogist-Transposer.obj: fvlib/Transposer.cpp
+ at am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -MT fvlib/palogist-Transposer.obj -MD -MP -MF fvlib/$(DEPDIR)/palogist-Transposer.Tpo -c -o fvlib/palogist-Transposer.obj `if test -f 'fvlib/Transposer.cpp'; then $(CYGPATH_W) 'fvlib/Transposer.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/Transposer.cpp'; fi`
+ at am__fastdepCXX_TRUE@ $(AM_V_at)$(am__mv) fvlib/$(DEPDIR)/palogist-Transposer.Tpo fvlib/$(DEPDIR)/palogist-Transposer.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@ $(AM_V_CXX)source='fvlib/Transposer.cpp' object='fvlib/palogist-Transposer.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -c -o palogist-Transposer.obj `if test -f 'fvlib/Transposer.cpp'; then $(CYGPATH_W) 'fvlib/Transposer.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/Transposer.cpp'; fi`
+ at am__fastdepCXX_FALSE@ $(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -c -o fvlib/palogist-Transposer.obj `if test -f 'fvlib/Transposer.cpp'; then $(CYGPATH_W) 'fvlib/Transposer.cpp'; else $(CYGPATH_W) '$(srcdir)/fvlib/Transposer.cpp'; fi`
palogist-eigen_mematrix.o: eigen_mematrix.cpp
@am__fastdepCXX_TRUE@ $(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(palogist_CPPFLAGS) $(CPPFLAGS) $(palogist_CXXFLAGS) $(CXXFLAGS) -MT palogist-eigen_mematrix.o -MD -MP -MF $(DEPDIR)/palogist-eigen_mematrix.Tpo -c -o palogist-eigen_mematrix.o `test -f 'eigen_mematrix.cpp' || echo '$(srcdir)/'`eigen_mematrix.cpp
@@ -2108,6 +2067,8 @@ clean-generic:
distclean-generic:
-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+ -rm -f fvlib/$(DEPDIR)/$(am__dirstamp)
+ -rm -f fvlib/$(am__dirstamp)
maintainer-clean-generic:
@echo "This command is intended for maintainers to use"
@@ -2117,7 +2078,7 @@ clean: clean-am
clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
distclean: distclean-am
- -rm -rf ./$(DEPDIR)
+ -rm -rf ./$(DEPDIR) fvlib/$(DEPDIR)
-rm -f Makefile
distclean-am: clean-am distclean-compile distclean-generic \
distclean-hdr distclean-tags
@@ -2166,7 +2127,7 @@ install-ps-am:
installcheck-am:
maintainer-clean: maintainer-clean-am
- -rm -rf ./$(DEPDIR)
+ -rm -rf ./$(DEPDIR) fvlib/$(DEPDIR)
-rm -f Makefile
maintainer-clean-am: distclean-am maintainer-clean-generic
diff --git a/src/command_line_settings.cpp b/src/command_line_settings.cpp
index 33bd1c3..34a4103 100644
--- a/src/command_line_settings.cpp
+++ b/src/command_line_settings.cpp
@@ -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>
diff --git a/src/command_line_settings.h b/src/command_line_settings.h
index f53c913..f5bcdd8 100644
--- a/src/command_line_settings.h
+++ b/src/command_line_settings.h
@@ -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>
diff --git a/src/coxph_data.cpp b/src/coxph_data.cpp
index 9ffc15d..0d0495d 100644
--- a/src/coxph_data.cpp
+++ b/src/coxph_data.cpp
@@ -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>
diff --git a/src/coxph_data.h b/src/coxph_data.h
index aa55d56..87cb569 100644
--- a/src/coxph_data.h
+++ b/src/coxph_data.h
@@ -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_
diff --git a/src/data.cpp b/src/data.cpp
index 0b3aa09..662e67e 100644
--- a/src/data.cpp
+++ b/src/data.cpp
@@ -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>
diff --git a/src/data.h b/src/data.h
index 3375ea1..20e190b 100644
--- a/src/data.h
+++ b/src/data.h
@@ -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>
diff --git a/src/eigen_mematrix.cpp b/src/eigen_mematrix.cpp
index ff910c2..4470c5f 100644
--- a/src/eigen_mematrix.cpp
+++ b/src/eigen_mematrix.cpp
@@ -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"
@@ -185,12 +208,12 @@ void mematrix<DT>::reinit(int nr, int nc)
// delete[] data;
if (nr <= 0)
{
- std::cerr << "mematrix(): number of rows smaller then 1\n";
+ std::cerr << "mematrix(): number of rows less than 1\n";
exit(1);
}
if (nc <= 0)
{
- std::cerr << "mematrix(): number of columns smaller then 1\n";
+ std::cerr << "mematrix(): number of columns less than 1\n";
exit(1);
}
nrow = nr;
@@ -373,7 +396,7 @@ void mematrix<DT>::delete_column(const int delcol)
exit(1);
}
- MatrixXd auxdata = data;
+ Matrix<DT, Dynamic, Dynamic, RowMajor> auxdata = data;
data.resize(data.rows(), data.cols()-1);
int rightColsSize = auxdata.cols() - delcol - 1;
@@ -394,8 +417,7 @@ void mematrix<DT>::delete_row(const int delrow)
exit(1);
}
-
- MatrixXd auxdata = data;
+ Matrix<DT, Dynamic, Dynamic, RowMajor> auxdata = data;
data.resize(data.rows()-1, data.cols());
int bottomRowsSize = auxdata.rows() - delrow - 1;
diff --git a/src/eigen_mematrix.h b/src/eigen_mematrix.h
index f671998..3503ab0 100644
--- a/src/eigen_mematrix.h
+++ b/src/eigen_mematrix.h
@@ -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>
diff --git a/src/gendata.cpp b/src/gendata.cpp
index d43e2af..a1442e9 100644
--- a/src/gendata.cpp
+++ b/src/gendata.cpp
@@ -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"
@@ -30,6 +52,8 @@ void gendata::get_var(int var, double * data)
}
else if (DAG != NULL) // Read from fv file
{
+ // cout << "Data Type: " << dataTypeToString(DAG->getElementType())
+ // << endl;
double *tmpdata = new double[DAG->getNumObservations()];
DAG->readVariableAs((unsigned long int) var, tmpdata);
@@ -41,14 +65,14 @@ void gendata::get_var(int var, double * data)
// A dirty trick to get rid of conversion
// errors. Instead of casting float data to double we
// convert the data to string and then do strtod()
- std::ostringstream strs;
- strs << tmpdata[i];
- std::string str = strs.str();
+ char tmpstr[1048576];
+ snprintf (tmpstr, sizeof(tmpstr), "%f", tmpdata[i]);
+
double val;
char *endptr;
errno = 0; // To distinguish success/failure
// after strtod()
- val = strtod(str.c_str(), &endptr);
+ val = strtod(tmpstr, &endptr);
if ((errno == ERANGE && (val == HUGE_VALF || val == HUGE_VALL))
|| (errno != 0 && val == 0)) {
@@ -56,7 +80,7 @@ void gendata::get_var(int var, double * data)
exit(EXIT_FAILURE);
}
- if (endptr == str.c_str()) {
+ if (endptr == tmpstr) {
cerr << "No digits were found while reading genetic data"
<< " (individual " << i + 1
<< ", position " << var + 1 << ")"
@@ -193,8 +217,9 @@ void gendata::re_gendata(char * fname, unsigned int insnps,
if (infile.good())
{
infile >> tmpstr;
- // tmpstr contains the dosage in string form. Convert
- // it to double (if tmpstr is NaN it will be set to nan).
+ // tmpstr contains the dosage/probability in
+ // string form. Convert it to double (if tmpstr is
+ // NaN it will be set to nan).
double dosage;
char *endptr;
errno = 0; // To distinguish success/failure
diff --git a/src/gendata.h b/src/gendata.h
index 13b62e7..079cd8d 100644
--- a/src/gendata.h
+++ b/src/gendata.h
@@ -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>
diff --git a/src/main.cpp b/src/main.cpp
index 57d145f..5543c90 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -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>
diff --git a/src/main_functions_dump.cpp b/src/main_functions_dump.cpp
index fcd7601..f2e78fb 100644
--- a/src/main_functions_dump.cpp
+++ b/src/main_functions_dump.cpp
@@ -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.
+ *
*/
diff --git a/src/main_functions_dump.h b/src/main_functions_dump.h
index 3f75cda..a590136 100644
--- a/src/main_functions_dump.h
+++ b/src/main_functions_dump.h
@@ -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_
diff --git a/src/maskedmatrix.cpp b/src/maskedmatrix.cpp
index f5d90de..a696ab2 100644
--- a/src/maskedmatrix.cpp
+++ b/src/maskedmatrix.cpp
@@ -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"
diff --git a/src/maskedmatrix.h b/src/maskedmatrix.h
index c594640..4470d10 100644
--- a/src/maskedmatrix.h
+++ b/src/maskedmatrix.h
@@ -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_
diff --git a/src/mematri1.h b/src/mematri1.h
index 43817a9..b80c3dc 100644
--- a/src/mematri1.h
+++ b/src/mematri1.h
@@ -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
diff --git a/src/mematrix.h b/src/mematrix.h
index 700e6ed..e9b0d93 100644
--- a/src/mematrix.h
+++ b/src/mematrix.h
@@ -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>
diff --git a/src/phedata.cpp b/src/phedata.cpp
index 4c0bc18..9f7426b 100644
--- a/src/phedata.cpp
+++ b/src/phedata.cpp
@@ -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>
diff --git a/src/phedata.h b/src/phedata.h
index c35aa73..13d0687 100644
--- a/src/phedata.h
+++ b/src/phedata.h
@@ -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_
diff --git a/src/reg1.cpp b/src/reg1.cpp
index a7062ac..1c85e0b 100644
--- a/src/reg1.cpp
+++ b/src/reg1.cpp
@@ -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"
@@ -696,7 +719,8 @@ void logistic_reg::estimate(regdata& rdatain, int verbose, int maxiter,
double emu = eMu.get(i, 0);
double value = emu;
double zval;
- value = exp(value) / (1. + exp(value));
+ double expval = exp(value);
+ value = expval / (1. + expval);
residuals[i] = (rdata.Y).get(i, 0) - value;
eMu.put(value, i, 0);
W.put(value * (1. - value), i, 0);
@@ -755,11 +779,13 @@ void logistic_reg::estimate(regdata& rdatain, int verbose, int maxiter,
beta.print();
}
// std::cout << "beta:\n"; beta.print();
- // compute likelihood
+
+ // Compute the likelihood.
prevlik = loglik;
- loglik = 0.;
- for (int i = 0; i < eMu.nrow; i++)
+ loglik = 0;
+ for (int i = 0; i < eMu.nrow; i++) {
loglik += rdata.Y[i] * eMu_us[i] - log(1. + exp(eMu_us[i]));
+ }
delta = fabs(1. - (prevlik / loglik));
niter++;
diff --git a/src/reg1.h b/src/reg1.h
index 02b646e..8e98810 100644
--- a/src/reg1.h
+++ b/src/reg1.h
@@ -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_
diff --git a/src/regdata.cpp b/src/regdata.cpp
index d09682c..f3e6613 100644
--- a/src/regdata.cpp
+++ b/src/regdata.cpp
@@ -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"
@@ -125,6 +146,7 @@ void regdata::update_snp(gendata *gend, const int snpnum)
for (int i = 0; i < nids; i++) {
X.put(snpdata[i], i, (ncov - j));
+
if (std::isnan(snpdata[i])) {
masked_data[i] = 1;
// SNP not masked
diff --git a/src/regdata.h b/src/regdata.h
index e124d4c..9d28dd5 100644
--- a/src/regdata.h
+++ b/src/regdata.h
@@ -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.
+ *
*/
+
#ifndef REGDATA_H_
#define REGDATA_H_
diff --git a/src/usage.cpp b/src/usage.cpp
index ce13f1a..d57e79d 100644
--- a/src/usage.cpp
+++ b/src/usage.cpp
@@ -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 <iostream>
#include <fstream>
#include <cstdlib>
@@ -77,8 +100,8 @@ void print_usage(char * program_name, int exit_code)
void print_version(void) {
cout << PACKAGE
<< " v. " << PACKAGE_VERSION
- << "\n(C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, "
- << "EMCR\n\n";
+ << "\n(C) Yurii Aulchenko, Lennart C. Karssen, Maarten Kooyman, "
+ << "Maksim Struchalin, The GenABEL team, EMC Rotterdam\n\n";
#if EIGEN
cout << "Using EIGEN version " << EIGEN_WORLD_VERSION
<< "." << EIGEN_MAJOR_VERSION << "." << EIGEN_MINOR_VERSION
diff --git a/src/usage.h b/src/usage.h
index b6be61e..4738cd3 100644
--- a/src/usage.h
+++ b/src/usage.h
@@ -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 USAGE_H_
#define USAGE_H_
void print_usage(char * program_name, int exit_code);
diff --git a/src/utilities.cpp b/src/utilities.cpp
index 437da3f..9b2129d 100644
--- a/src/utilities.cpp
+++ b/src/utilities.cpp
@@ -3,7 +3,29 @@
*
* Created on: Mar 15, 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 <cstdarg>
#include <cstdio>
diff --git a/src/utilities.h b/src/utilities.h
index 8057129..fb99a69 100644
--- a/src/utilities.h
+++ b/src/utilities.h
@@ -3,8 +3,29 @@
*
* Created on: Mar 15, 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 UTILITIES_H_
#define UTILITIES_H_
void report_error(const char * format, ...);
--
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