[Genabel-commits] r759 - in pkg/ProbABEL: doc src

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2011-08-12 10:06:43 +0200 (Fri, 12 Aug 2011)
New Revision: 759

Removed:
   pkg/ProbABEL/src/version.h
Modified:
   pkg/ProbABEL/doc/ProbABEL_manual.tex
   pkg/ProbABEL/src/Makefile.am
   pkg/ProbABEL/src/Makefile.in
   pkg/ProbABEL/src/main.cpp
Log:
- Fixed bug $1290: usage of DatABEL files not explained in the
  manual. See also http://forum.genabel.org/viewtopic.php?f=6&t=22 for
  some discussion.
- Since we now use autoconf, which generates src/config.h, we don't
  need a separate src/version.h anymore. When upgrading the version of
  ProbABEL, simply do it in configure.ac and the change will be
  automatically trickle down to main.cpp.



Modified: pkg/ProbABEL/doc/ProbABEL_manual.tex
===================================================================
--- pkg/ProbABEL/doc/ProbABEL_manual.tex	2011-08-11 22:41:45 UTC (rev 758)
+++ pkg/ProbABEL/doc/ProbABEL_manual.tex	2011-08-12 08:06:43 UTC (rev 759)
@@ -93,13 +93,6 @@
 Optionally, the map information can be supplied (e.g.~the "legend"
 files of HapMap).
 
-The dose/probbaility file may be supplied in filevector format
-in which case \texttt{ProbABEL} will operate much faster, and
-in low-RAM mode (approx.~128 MB). See the R libraries GenABEL and
-DatABEL on how to convert MACH and IMPUTE files to
-filevector format (functions: \texttt{mach2databel()} and
-\texttt{impute2databel()}, respectively).
-
 \subsection{SNP information file}
 \label{ssec:infoin}
 In the simplest scenario, the SNP information file is an MLINFO
@@ -149,6 +142,18 @@
 Therefore, by all means, the number of columns in the genomic predictor file
 must be the same as the number of lines in the SNP information file plus one.
 
+The dose/probability file may be supplied in filevector format
+(\texttt{.fvi} and \texttt{.fvd} files) in which case
+\texttt{ProbABEL} will operate much faster, and in low-RAM mode
+(approx.~128 MB). On the command line simply specify the \texttt{.fvi}
+file as argument for the \texttt{--dose} option
+(cf.~section~\ref{sec:runanalysis} for more information on the options
+accepted by \texttt{ProbABEL}). See the R libraries GenABEL and
+DatABEL on how to convert MACH and IMPUTE files to filevector format
+(functions: \texttt{mach2databel()} and \texttt{impute2databel()},
+respectively).
+
+
 \subsection{Phenotypic file}
 \label{ssec:phenoin}
 
@@ -226,6 +231,7 @@
 actually used to generate the output.
 
 \section{Running an analysis}
+\label{sec:runanalysis}
 To run linear regression, you should use the program called
 \texttt{palinear}; for logistic analysis use \texttt{palogist}, and
 for the Cox proportional hazards model use \texttt{pacoxph} (all are

Modified: pkg/ProbABEL/src/Makefile.am
===================================================================
--- pkg/ProbABEL/src/Makefile.am	2011-08-11 22:41:45 UTC (rev 758)
+++ pkg/ProbABEL/src/Makefile.am	2011-08-12 08:06:43 UTC (rev 759)
@@ -3,7 +3,7 @@
 ## Using wildcards in these lists doesn't work. Also GNU make's ($wildcard,) doesn't
 ## work. It gives warning message about portability, but in the end doesn't work,
 ## I tried :-).
-REGFILES = data.h mematrix.h reg1.h usage.h main.cpp mematri1.h version.h
+REGFILES = data.h mematrix.h reg1.h usage.h main.cpp mematri1.h
 
 ## Filevector files:
 FVSRC = fvlib/AbstractMatrix.cpp fvlib/CastUtils.cpp			\

Modified: pkg/ProbABEL/src/Makefile.in
===================================================================
--- pkg/ProbABEL/src/Makefile.in	2011-08-11 22:41:45 UTC (rev 758)
+++ pkg/ProbABEL/src/Makefile.in	2011-08-12 08:06:43 UTC (rev 759)
@@ -234,7 +234,7 @@
 top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
-REGFILES = data.h mematrix.h reg1.h usage.h main.cpp mematri1.h version.h
+REGFILES = data.h mematrix.h reg1.h usage.h main.cpp mematri1.h
 FVSRC = fvlib/AbstractMatrix.cpp fvlib/CastUtils.cpp			\
  fvlib/convert_util.cpp fvlib/FileVector.cpp fvlib/FilteredMatrix.cpp	\
  fvlib/frutil.cpp fvlib/Logger.cpp fvlib/RealHandlerWrapper.cpp		\

Modified: pkg/ProbABEL/src/main.cpp
===================================================================
--- pkg/ProbABEL/src/main.cpp	2011-08-11 22:41:45 UTC (rev 758)
+++ pkg/ProbABEL/src/main.cpp	2011-08-12 08:06:43 UTC (rev 759)
@@ -9,7 +9,8 @@
 //           Revision:  none
 //
 //             Author:  Yurii S. Aulchenko (cox, log, lin regressions)
-//             Modified by: Maksim V. Struchalin, 
+//             Modified by: L.C. Karssen,
+//                          Maksim V. Struchalin
 // 
 // modified 14-May-2009 by MVS: interaction with SNP, interaction with SNP with exclusion of interacted covariates,
 //                              mmscore implemented (poor me)
@@ -38,7 +39,7 @@
 #include <sstream>
 
 
-#include "version.h"
+#include "config.h"
 #include "mematrix.h"
 #include "mematri1.h"
 #include "data.h"
@@ -184,7 +185,11 @@
 	while (next_option != -1);
 
 
-	fprintf(stdout,"ProbABEL v. %s (%s) (C) Yurii Aulchenko, Maksim Struchalin, EMCR\n\n",VERSION,DATE);
+	fprintf(stdout, 
+		"%s v. %s (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR\n\n", 
+		PACKAGE, 
+		PACKAGE_VERSION);
+
 	if (neco[0]!=1 || neco[1]!=1 || neco[2]!=1)
 	{
 		print_usage(program_name,1);

Deleted: pkg/ProbABEL/src/version.h
===================================================================
--- pkg/ProbABEL/src/version.h	2011-08-11 22:41:45 UTC (rev 758)
+++ pkg/ProbABEL/src/version.h	2011-08-12 08:06:43 UTC (rev 759)
@@ -1,2 +0,0 @@
-#define VERSION "0.1-9e"
-#define DATE "May 15, 2011"