1 files changed, 138 insertions, 7 deletions

diff --git a/src/debug.cpp b/src/debug.cpp
index 0d3c9cc..fd94f1e 100644
--- a/src/debug.cpp
+++ b/src/debug.cpp
@@ -1,3 +1,22 @@
+/*
+    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>
@@ -18,28 +37,140 @@
 #include "debug.h"
 #include "mathfunc.h"
 
-// Helper function called by macro validate_K(K, check)
-void do_validate_K(const gsl_matrix *K, bool do_check, bool strict, const char *__file, int __line) {
-  if (do_check) {
+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_small_values(eigenvalues,EIGEN_MINVALUE);
+    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))
+    if (isMatrixIllConditioned(eigenvalues))
       warning_at_msg(__file,__line,"K is ill conditioned!");
     if (!isMatrixSymmetric(K))
-      fail_at_msg(strict,__file,__line,"K is not symmetric!" );
+      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))
-      fail_at_msg(strict,__file,__line,"K is not positive definite!");
+      warnfail_at_msg(is_strict_mode(),__pretty_function,__file,__line,"K is not positive definite!");
     gsl_vector_free(eigenvalues);
   }
 }