Commit e3b45c83 authored by Damien Leroux's avatar Damien Leroux
Browse files

Updated settings to include basic pipeline configuration.

parent 3593ef62
......@@ -6,7 +6,8 @@
#include "input/read_trait.h"
#include "input/design.h"
#include <exception>
#include <Eigen/Core>
/*#include <Eigen/Core>*/
#include "eigen.h"
#include "proba_config.h"
#include "generation_rs.h"
......@@ -55,23 +56,33 @@ struct settings_t {
std::string epistasis_qtl_selection_filename;
std::map<std::string, double> qtl_thresholds;
int n_permutations;
double qtl_threshold_quantile;
std::map<std::string, double> cofactor_thresholds;
std::string skeleton_mode;
std::vector<std::string> skeleton_markers;
double skeleton_interval;
std::string cofactor_algorithm;
std::string qtl_algorithm;
#if 0
enum class detection_method_t : char {
Undef,
iQTLm,
CIM
};
std::map<std::string, double> qtl_thresholds;
int n_permutations;
double qtl_threshold_quantile;
double cofactor_threshold;
bool P_required;
bool T_required;
bool E_required;
bool D_required;
detection_method_t detection_method;
double detection_window;
#endif
ThreadPool* pool;
static std::thread::id main_thread;
......@@ -91,7 +102,7 @@ struct settings_t {
, working_set()
, step(1)
, parallel(0)
, work_directory()
, work_directory("/tmp")
, connected(false)
, epistasis(false)
, pleiotropy(false)
......@@ -103,9 +114,14 @@ struct settings_t {
, qtl_thresholds()
, n_permutations(10000)
, qtl_threshold_quantile(0.05)
, cofactor_threshold(0)
, detection_method(detection_method_t::Undef)
, detection_window(10.)
, cofactor_thresholds()
, skeleton_mode("auto")
, skeleton_markers()
, skeleton_interval(20.)
, cofactor_algorithm("forward")
, qtl_algorithm("iQTLm")
/*, detection_method(detection_method_t::Undef)*/
/*, detection_window(10.)*/
, pool(0)
, tolerance(1.e-10)
, estimation_loci()
......@@ -209,8 +225,8 @@ struct settings_t {
{
if (pool && msg_handler_t::color()) {
pool->set_title(t);
/*} else {*/
/*MSG_INFO("Current task: " << t);*/
} else {
MSG_INFO("Current task: " << t);
}
}
......
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