Commit 7f7115af authored by Andreas Tille's avatar Andreas Tille

Drop unused patches, add patch to comply with C++11

parent f0d286b6
Origin: https://github.com/GenABEL-Project/ProbABEL/commit/2267200e76b29c6e7fa431df3e5abaf2879e2fc1
Author: L.C. Karssen <lennart@karssen.org>
Date: Tue Dec 6 15:55:16 2016 +0100
Description: Fix compiler errors about static const double on GCC 6.2.0
This fixes issue #32.
.
See e.g.
https://en.wikipedia.org/wiki/C%2B%2B11#constexpr_.E2.80.93_Generalized_constant_expressions
and http://en.cppreference.com/w/cpp/language/constexpr
--- a/src/coxph_data.h
+++ b/src/coxph_data.h
@@ -220,13 +220,13 @@ class coxph_reg {
* Iteration continues until the percent change in loglikelihood
* is <= EPS.
*/
- static const double EPS = 1e-9;
+ static constexpr double EPS = 1e-9;
/**
* \brief Constant containing the precision for the Cholesky
* decomposition.
*/
- static const double CHOLTOL = 1.5e-12;
+ static constexpr double CHOLTOL = 1.5e-12;
};
#endif /* COXPH_DATA_H_ */
--- a/src/reg1.h
+++ b/src/reg1.h
@@ -185,7 +185,7 @@ class logistic_reg: public base_reg {
* Iteration continues until the percent change in loglikelihood
* is <= EPS.
*/
- static const double EPS = 1e-8;
+ static constexpr double EPS = 1e-8;
};
#endif // REG1_H_
Description: Don't install the checks that are run by 'make check'
Having these checks installed is of no use to a regular user.
Author: L.C. Karssen <lennart@karssen.org>
Forwarded: no
Last-Update: 2013-12-16
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- a/checks/Makefile.am
+++ b/checks/Makefile.am
@@ -57,9 +57,9 @@
TESTS = $(check_SCRIPTS)
-testsdir = $(pkgdatadir)/tests
-dist_tests_DATA = $(verified_results) $(input_files)
-dist_tests_SCRIPTS = $(check_SCRIPTS)
+#testsdir = $(pkgdatadir)/tests
+#dist_tests_DATA = $(verified_results) $(input_files)
+#dist_tests_SCRIPTS = $(check_SCRIPTS)
##################################################
Description: Fix Makefile.am to install extIDS.pl in a more appropriate location.
This patch will be sent upstream.
Author: L.C. Karssen <lennart@karssen.org>
Forwarded: TODO
Last-Update: 2013-12-12
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -74,12 +74,12 @@
extract_snp_SOURCES = extract-snp.cpp $(FVSRC) $(FVHEADERS)
-## Install these scripts in the bin directory as well:
-dist_bin_SCRIPTS = probabel.pl extIDS.pl
+## Install the wrapper script in the bin directory as well:
+dist_bin_SCRIPTS = probabel.pl
-## Install this R script in the examples directory
+## Install these scripts in the examples directory
scriptdir = $(pkgdatadir)/scripts
-dist_script_DATA = prepare_data.R
+dist_script_DATA = prepare_data.R extIDS.pl
## Install the config file
dist_sysconf_DATA = probabel_config.cfg.example
Description: Change the shell used in one of the checks.
One of the checks has /bin/sh as interpreter, but uses bashisms, therefore the interpreter should be /bin/bash
Author: L.C. Karssen <lennart@karssen.org>
Origin: upstream
Forwarded: not-needed
Last-Update: 2013-12-13
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- a/checks/check_dose_input.sh
+++ b/checks/check_dose_input.sh
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
#
# This script tests whether dose data without a MaCH/minimac-style
# arrow is read correctly by palinear (and by palogist, since reading
Description: Fix the checks, which failed after running dh_autoreconf
Automake v1.13 uses parallel test by default, unlike previous
versions. This patch runs tests the old serial way.
No need to forward upstream, upstream fixed this differently in SVN r1464.
Author: L.C. Karssen <lennart@karssen.org>
Last-Update: 2013-12-12
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- a/checks/Makefile.am
+++ b/checks/Makefile.am
@@ -41,7 +41,6 @@
check_SCRIPTS =
-TESTS_ENVIRONMENT = bash
if BUILD_palinear
check_SCRIPTS += check_probabel.pl_chunk.sh check_dose_input.sh
check_SCRIPTS += test_qt.sh test_mms.sh
--- a/configure.ac
+++ b/configure.ac
@@ -3,7 +3,7 @@
AC_PREREQ([2.67])
AC_INIT(ProbABEL, 0.4.1, genabel-devel@r-forge.wu-wien.ac.at)
-AM_INIT_AUTOMAKE([silent-rules])
+AM_INIT_AUTOMAKE([silent-rules serial-tests])
AM_SILENT_RULES
AC_CONFIG_SRCDIR([src/data.h])
AC_CONFIG_HEADERS([src/config.h])
Description: Add man-page for probabel.pl
This patch will be sent upstream.
Forwarded: TODO
Author: Lennart C. Karssen <lennart@karssen.org>
Last-Update: 2013-12-12
--- /dev/null
+++ b/doc/probabel.pl.1
@@ -0,0 +1,73 @@
+.TH probabel.pl 1 "12 December 2013"
+.SH NAME
+probabel.pl \- Wrapper around the three ProbABEL binaries, simplifying their use
+.SH SYNOPSIS
+.B probabel.pl
+.BI "" "CHROM-START CHROM-STOP METHOD COHORT MODEL PHENOTYPE [OTHER_OPTIONS]"
+.SH DESCRIPTION
+.B probabel.pl
+is a wrapper around the three ProbABEL binaries: \fBpalinear\fR,
+\fBpalogist\fR, and \fBpacoxph\fR.
+.PP
+It is designed to simplify runnig of a Genome-Wide Association Study
+(GWAS) by saving the user's precious time in two ways:
+.PP
+1) it runs the regression analysis of all chromosomes from \fICHROM-START\fR to
+\fICHROM-STOP\fR.
+.PP
+2) In contrast to the three binaries mentioned above,
+with \fBprobabel.pl\fR the user doesn't need to specify the locations
+of the required genetic data files. Their location is centrally
+managed in a configuration file (\fI/etc/probabel_config.cfg\fR by default).
+
+.SH OPTIONS
+.SS Required command line options
+.TP
+.I CHROM-START
+Number of the chromosome to start the analysis at.
+.TP
+.I CHROM-END
+Number of the chromosome to end the analysis at.
+.PP
+Note that analysis of a single chromosome can be run by specifying the
+same number for \fICHROM-START\fR and \fICHROM-STOP\fR. In fact, this
+is the way to run analysis for the X or Y chromosome
+.TP
+.I METHOD
+Which regression method to use, can be one of \fIlinear\fR,
+\fIlogistic,\fR or \fIcoxph\fR.
+
+.TP
+.I COHORT
+The name of the cohort as defined in the
+\fI/etc/probabel_config.cfg\fR file. Using the cohort identifier from
+the config file the three actual ProbABEL binaries know where to find
+the genotypic information files (dosage files and/or probability
+files).
+.TP
+.I MODEL
+The genetic model to be used. Can be either \fB--additive\fR for the
+additive model (requires genotype data in dosage form), or
+\fB--allmodels\fR to run all genetic models: additive, recessive,
+dominant, over-dominant and 2df.
+.TP
+.I PHENOTYPE
+The name of the phenotype file, without its extension (which should be
+\fI.PHE\fR!).
+
+.SS Other options
+Any options listed after the (mandatory) previous ones will be passed
+on to the underlying binary: \fBpalinear\fR, \fBpalogist\fR or
+\fBpacoxph\fR, depending on the \fIMETHOD\fR.
+.PP
+The most commonly used option is the \fB\-o\fR option, followed by a
+file name, this specifies the beginning of the file name for the
+output files.
+
+.SS Additional options
+.B "\-h, \-\-help"
+Get additional help on how to run \fBprobabel.pl\fR. In this case none of
+the other options needs to be specified.
+
+.SH EXAMPLES
+probabel.pl 1 22 linear "My_Large_Cohort" \-\-additive my_phenotype
--- a/doc/Makefile.am
+++ b/doc/Makefile.am
@@ -6,7 +6,7 @@
test.mlinfo test_regression.R COPYING LICENSE INSTALL ChangeLog \
TODO
-man_MANS =
+man_MANS = probabel.pl.1
if BUILD_palinear
man_MANS += palinear.1
endif
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