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/*
Genome-wide Efficient Mixed Model Association (GEMMA)
Copyright © 2011-2017, Xiang Zhou
Copyright © 2017, Peter Carbonetto
Copyright © 2017, Pjotr Prins
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 3 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, see <http://www.gnu.org/licenses/>.
*/
#include <cmath>
#include <cstring>
#include <ctime>
#include <fstream>
#include <iostream>
#include <string>
#include <sys/stat.h>
#include <vector>
#include "gsl/gsl_blas.h"
#include "gsl/gsl_cdf.h"
#include "gsl/gsl_eigen.h"
#include "gsl/gsl_linalg.h"
#include "gsl/gsl_matrix.h"
#include "gsl/gsl_vector.h"
#include "debug.h"
#include "mathfunc.h"
static bool debug_mode = false;
static bool debug_check = true; // check data/algorithms
static bool debug_strict = false; // fail on error, more rigorous checks
static bool debug_quiet = false;
static uint debug_issue = 0; // track github issues
static bool debug_legacy = false; // legacy mode
void debug_set_debug_mode(bool setting) { debug_mode = setting; }
void debug_set_no_check_mode(bool setting) {debug_check = !setting; }
void debug_set_strict_mode(bool setting) { debug_strict = setting; }
void debug_set_quiet_mode(bool setting) { debug_quiet = setting; }
void debug_set_issue(uint issue) { debug_issue = issue; }
void debug_set_legacy_mode(bool setting) { debug_legacy = setting; }
bool is_debug_mode() { return debug_mode; };
bool is_no_check_mode() { return !debug_check; };
bool is_check_mode() { return debug_check; };
bool is_strict_mode() { return debug_strict; };
bool is_quiet_mode() { return debug_quiet; };
bool is_issue(uint issue) { return issue == debug_issue; };
bool is_legacy_mode() { return debug_legacy; };
/*
Helper function to make sure gsl allocations do their job because
gsl_matrix_alloc does not initiatize values (behaviour that changed
in GSL2) we introduced a 'strict mode' by initializing the buffer
with NaNs. This happens when NO-CHECKS is not set (default) and with
DEBUG (i.e. -debug option).
*/
gsl_matrix *gsl_matrix_safe_alloc(size_t rows,size_t cols) {
gsl_matrix *m = gsl_matrix_alloc(rows,cols);
enforce_msg(m,"Not enough memory"); // just to be sure when there is no error handler set
if (is_check_mode() && is_debug_mode()) {
gsl_matrix_set_all(m, nan(""));
}
return m;
}
int gsl_matrix_safe_memcpy (gsl_matrix *dest, const gsl_matrix *src) {
enforce(dest->size1 == src->size1);
enforce(dest->size2 == src->size2);
return gsl_matrix_memcpy(dest,src);
}
void do_gsl_matrix_safe_free (gsl_matrix *m, const char *__pretty_function, const char *__file, int __line) {
enforce(m);
if (is_strict_mode() && is_check_mode() && is_debug_mode()) {
bool has_NaN = has_nan(m);
bool has_Inf = has_inf(m);
if (has_NaN || has_Inf) {
std::string msg = "Matrix (size ";
msg += std::to_string(m->size1);
msg += "x";
msg += std::to_string(m->size2);
msg += ")";
if (has_Inf)
warnfail_at_msg(is_strict_mode(),__pretty_function,__file,__line,(msg+" contains Infinite on free!").c_str());
if (has_NaN)
warnfail_at_msg(is_strict_mode(),__pretty_function,__file,__line,(msg+" contains NaN on free!").c_str());
}
}
return gsl_matrix_free(m);
}
int gsl_vector_safe_memcpy (gsl_vector *dest, const gsl_vector *src) {
enforce(dest->size == src->size);
return gsl_vector_memcpy(dest,src);
}
void do_gsl_vector_safe_free (gsl_vector *v, const char *__pretty_function, const char *__file, int __line) {
enforce(v);
if (is_strict_mode() && is_check_mode() && is_debug_mode()) {
bool has_NaN = has_nan(v);
bool has_Inf = has_inf(v);
if (has_NaN || has_Inf) {
std::string msg = "Vector (size ";
msg += std::to_string(v->size);
msg += ")";
if (has_Inf)
warnfail_at_msg(is_strict_mode(),__pretty_function,__file,__line,(msg+" contains Infinite on free!").c_str());
if (has_NaN)
warnfail_at_msg(is_strict_mode(),__pretty_function,__file,__line,(msg+" contains NaN on free!").c_str());
}
}
return gsl_vector_free(v);
}
/*
Helper function to make sure gsl allocations do their job because
gsl_vector_alloc does not initiatize values (behaviour that changed
in GSL2) we introduced a 'strict mode' by initializing the buffer
with NaNs. This happens when NO-CHECKS is not set and with DEBUG
(i.e. -debug option).
*/
gsl_vector *gsl_vector_safe_alloc(size_t n) {
gsl_vector *v = gsl_vector_alloc(n);
enforce_msg(v,"Not enough memory"); // just to be sure when there is no error handler set
if (is_check_mode() && is_debug_mode()) {
gsl_vector_set_all(v, nan(""));
}
return v;
}
char *do_strtok_safe(char *tokenize, const char *delimiters, const char *__pretty_function, const char *__file, int __line) {
auto token = strtok(tokenize,delimiters);
if (token == NULL && (is_debug_mode() || is_strict_mode()))
fail_at_msg(__file,__line,string("strtok failed in ") + __pretty_function);
return token;
}
// Helper function called by macro validate_K(K, check). K is validated
// unless -no-check option is used.
void do_validate_K(const gsl_matrix *K, const char *__pretty_function, const char *__file, int __line) {
if (is_check_mode()) {
// debug_msg("Validating K");
auto eigenvalues = getEigenValues(K);
const uint count_small = count_abs_small_values(eigenvalues,EIGEN_MINVALUE);
if (count_small>1) {
std::string msg = "K has ";
msg += std::to_string(count_small);
msg += " eigenvalues close to zero";
warning_at_msg(__file,__line,msg);
}
if (isMatrixIllConditioned(eigenvalues))
warning_at_msg(__file,__line,"K is ill conditioned!");
if (!isMatrixSymmetric(K))
warnfail_at_msg(is_strict_mode(),__pretty_function,__file,__line,"K is not symmetric!" );
const bool negative_values = has_negative_values_but_one(eigenvalues);
if (negative_values) {
warning_at_msg(__file,__line,"K has more than one negative eigenvalues!");
}
if (count_small>1 && negative_values && !isMatrixPositiveDefinite(K))
warnfail_at_msg(is_strict_mode(),__pretty_function,__file,__line,"K is not positive definite!");
gsl_vector_free(eigenvalues);
}
}
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