Switched to eigen-3.3 and fixed behaviour when with_traits is empty.

include/bayes/output.h

@@ -1230,6 +1230,7 @@ struct pop_data_type {
                     ret[ti].P = traits[ti].P;
                     ret[ti].raw = reduce_with_good_indices(traits[ti].raw, traits[ti].good_indices, ret[ti].good_indices);
                     ret[ti].values = reduce_with_good_indices(traits[ti].values, traits[ti].good_indices, ret[ti].good_indices);
+                    ret[ti].dim_names = traits[ti].dim_names;
                 }
                 return ret;
             };

include/computations/frontends4.h

@@ -2386,9 +2386,9 @@ void analysis_report::report_final_model(model_manager& mm)
         report_file << std::string("* There are not enough observations to compute a variance/covariance matrix. Results not displayed.") << std::endl;
     } else {
         MatrixXd Pt = TM.P.transpose();
-        if (Pt.size() == 0) {
-            Pt = MatrixXd::Ones(1, 1);
-        }
+//         if (Pt.size() == 0) {
+//             Pt = MatrixXd::Ones(1, 1);
+//         }
 //         MSG_DEBUG(TM.P);
 //         MSG_DEBUG(MATRIX_SIZE(Pt));
 //         MSG_DEBUG(MATRIX_SIZE(mm.vMcurrent->coefficients()));

include/eigen.h

@@ -43,27 +43,27 @@ template <typename X> using SelfAdjointEigenSolver = Eigen::SelfAdjointEigenSolv
 #endif
 
 
-namespace Eigen {
-    template<>
-    struct NumTraits<std::string> {
-        typedef std::string Real;
-        typedef std::string NonInteger;
-        typedef std::string Nested;
-        enum {
-            IsComplex = 0,
-            IsInteger = 1,
-            ReadCost = 100,
-            WriteCost = 100,
-            MulCost = 1000,
-            IsSigned = 0,
-            RequireInitialization = 1
-        };
-        static Real epsilon() { return { std::string() }; }
-        static Real dummy_precision() { return { std::string() }; }
-        static std::string highest() { return std::string(); }
-        static std::string lowest() { return std::string(); }
-    };
-}
+// namespace Eigen {
+//     template<>
+//     struct NumTraits<std::string> {
+//         typedef std::string Real;
+//         typedef std::string NonInteger;
+//         typedef std::string Nested;
+//         enum {
+//             IsComplex = 0,
+//             IsInteger = 1,
+//             ReadCost = 100,
+//             WriteCost = 100,
+//             MulCost = 1000,
+//             IsSigned = 0,
+//             RequireInitialization = 1
+//         };
+//         static Real epsilon() { return { std::string() }; }
+//         static Real dummy_precision() { return { std::string() }; }
+//         static std::string highest() { return std::string(); }
+//         static std::string lowest() { return std::string(); }
+//     };
+// }
 
 
 

include/input/read_trait.h

@@ -215,7 +215,7 @@ namespace read_data {
 
 inline std::ostream& operator << (std::ostream& os, const trait& t)
 {
-    os << "<single_trait:" << t.name << ' ' << t.values.cols() << " dimensions, " << t.values.rows() << " values, ";
+    os << "<single_trait:" << t.name << ' ' << t.values.cols() << " dimensions, " << t.dim_names << ", " << t.values.rows() << " values, ";
 //    for (double v: t.values) {
 //        os << ' ' << v;
 //    }

include/linear_combination.h

@@ -931,6 +931,7 @@ namespace Eigen {
         typedef combination_type<PARENT_TYPE> Real;
         typedef combination_type<PARENT_TYPE> NonInteger;
         typedef combination_type<PARENT_TYPE> Nested;
+        typedef combination_type<PARENT_TYPE> Literal;
         enum {
             IsComplex = 0,
             IsInteger = 1,

include/settings.h

@@ -598,10 +598,16 @@ settings_t::finalize()
         MSG_ERROR("Some single traits are already used in pleiotropic traits: " << removed_traits, "Specify single trait names that are different from the trait names used in pleiotropic traits.");
         return;
     }
+    std::set<std::string> actual_single_traits;
     for (const auto& gt: datasets) {
         ifile ifs(gt.second);
         auto all_traits = read_data::read_trait(ifs, all_variables);
         auto observed_traits = assemble_traits(all_traits, with_traits, pleiotropic_traits_descr);
+        for (const auto& t: observed_traits) {
+            if (t.dim_names.size() == 1) {
+                actual_single_traits.insert(t.name);
+            }
+        }
         pop_data->set_qtl_generation(gt.first);
         MSG_DEBUG("with_covariables " << with_covariables);
         MSG_DEBUG("Creating covariables " << " from traits " << with_covariables << " in list " << observed_traits);
@@ -630,7 +636,7 @@ settings_t::finalize()
         trait_metadata[pleio.name].P = P;
         trait_metadata[pleio.name].dim_names = pleio.traits;
     }
-    for (const auto& t: with_traits) {
+    for (const auto& t: actual_single_traits) {
         trait_metadata[t].P = MatrixXd::Ones(1, 1);
         trait_metadata[t].dim_names = {t};
     }

src/input/read_trait.cc

@@ -70,9 +70,9 @@ std::vector<trait> read_trait(file& is, const std::vector<std::string>& filter_n
             ret.back().raw = ret.back().values;
             ret.back().P = MatrixXd::Ones(1, 1);
         }
-//        MSG_DEBUG("... read " << counter << " values (" << (counter - ret.back()->values.size()) << " missing)");
+       MSG_DEBUG("... read " << counter << " values (" << (counter - ret.back().values.size()) << " missing)");
     }
-    /*MSG_DEBUG("all traits " << ret);*/
+    MSG_DEBUG("all traits " << ret);
     return ret;
 }
 } /* namespace read_data */