Closes #7.

include/error.h

@@ -291,7 +291,7 @@ struct msg_handler_t {
             /*std::cout << "Message handler instance created." << std::endl;*/
         }
         ~state_t() { close_log_file(); }
-        void check(bool fatal);
+        bool check(bool fatal);
         void reset();
         void run_hooks() { for (auto& f: hooks) { f(); } }
         void close_log_file()
@@ -321,7 +321,7 @@ struct msg_handler_t {
     static const char* i() { return instance().info(); }
     static const char* n() { return instance().normal(); }
 
-    static void check(bool fatal) { instance().check(fatal); }
+    static bool check(bool fatal) { return instance().check(fatal); }
     static void reset() { instance().reset(); }
 
     static void hook(std::function<void()>&& f) { instance().hooks.push_back(f); }
@@ -703,7 +703,7 @@ struct scoped_indent {
 };
 
 
-inline void msg_handler_t::state_t::check(bool fatal)
+inline bool msg_handler_t::state_t::check(bool fatal)
 {
     msg_handler_t::scoped_lock_type _(msg_handler_t::mutex);
     if (count > 0) {
@@ -718,8 +718,10 @@ inline void msg_handler_t::state_t::check(bool fatal)
             exit(-count);
         } else {
             reset();
+            return true;
         }
     }
+    return false;
 }
 
 inline void msg_handler_t::state_t::reset()

include/pedigree.h

@@ -1473,6 +1473,18 @@ read_pedigree(const std::string& filename, char sep=';', size_t max_states=std::
     for (const auto& i: ret.items) {
         msg_handler_t::cout() << "\rProcessing entry " << (++cur) << "/" << ret.items.size() << " [" << i.id << ':' << i.p1 << ':' << i.p2 << "]...\x1b[K";
         MSG_QUEUE_FLUSH();
+        bool fail = false;
+        if (i.p1 != 0 && ret.m_id.find(i.p1) == ret.m_id.end()) {
+            MSG_ERROR("Unknown ID #" << i.p1 << " in pedigree", SPELL_STRING("Add individual #" << i.p1 << " to the pedigree file"));
+            fail = true;
+        }
+        if (i.p2 != 0 && ret.m_id.find(i.p2) == ret.m_id.end()) {
+            MSG_ERROR("Unknown ID #" << i.p2 << " in pedigree", SPELL_STRING("Add individual #" << i.p2 << " to the pedigree file"));
+            fail = true;
+        }
+        if (fail) {
+            return {};
+        }
         if (i.is_ancestor()) {
             ret.m_id[i.id] = ret.ancestor(i.gen_name);
         } else if (i.is_dh()) {

src/pedigree/main.cc

@@ -35,6 +35,9 @@ int SPELL_PEDIGREE_MAIN(int argc, const char** argv)
         print_usage();
     } else {
         pedigree_type ped = read_pedigree(settings->pedigree_filename, settings->csv_sep, settings->max_states);
+        if (!msg_handler_t::check(false)) {
+            return -1;
+        }
         std::string ped_output;
         if (settings->work_directory == "") {
             settings->work_directory = ".";

src/r-glue/spellmaptools.cc

@@ -61,8 +61,8 @@ public:
     EM(const marker_vec& order)
     { return gamete_LV.EM(order, m_convergence_threshold, m_max_iterations); }
     
-    void init_2pt_tr_at_inf() { gamete_LV.init_2pt_tr_at_inf(); }
-    double twoMarkerLikelihood(int i, double r) { return gamete_LV.twoMarkerLikelihood(i, r); }
+//     void init_2pt_tr_at_inf() { gamete_LV.init_2pt_tr_at_inf(); }
+    double twoMarkerLikelihood() { return gamete_LV.twoMarkerLikelihoodAtInf(); }
     
     int max_iterations(int n)
     {
@@ -129,7 +129,7 @@ public:
             double best = em.likelihood;
 //             instance->init_2pt_tr_at_inf();
 //             double inf_ref = instance->map_likelihood(minimap, at_worlds_end);
-            double inf_ref = instance->twoMarkerLikelihood(0, .5);
+            double inf_ref = instance->twoMarkerLikelihood();
             double value = best - inf_ref;
 //             MSG_INFO("LOD(" << minimap[0] << " … " << minimap[1] << " => d=" << em.distances[0] << " best=" << best << " inf_ref=" << inf_ref << " value=" << value);
             cache.emplace(key, value);
@@ -231,7 +231,11 @@ SpellMapTools::SpellMapTools(std::string ped_filename, Rwrap::DataFrame observat
 //         MSG_DEBUG(__FILE__ << ':' << __LINE__);
         data_time = std::time(nullptr);
         std::vector<std::string> args = {"spell-pedigree", "-wd", wd, "-n", name, "-p", ped_filename};
-        invoke_spell(SPELL_PEDIGREE_MAIN, args);
+        int ret = invoke_spell(SPELL_PEDIGREE_MAIN, args);
+        if (ret) {
+            MSG_ERROR("Something went wrong while loading the pedigree…", "");
+            return;
+        }
     } else {
 //         MSG_DEBUG(__FILE__ << ':' << __LINE__);
         data_time = spell_ped_t;
@@ -243,7 +247,7 @@ SpellMapTools::SpellMapTools(std::string ped_filename, Rwrap::DataFrame observat
 //     MSG_INFO("spell_mark_t=" << spell_mark_t);
 
     /* Run spell-marker if needed */
-    if (spell_mark_t < data_time) {
+    if (spell_mark_t < data_time && obs_gen.size() > 0) {
 //         MSG_DEBUG(__FILE__ << ':' << __LINE__);
         std::stringstream out;
         std::vector<std::string> args = {"spell-marker", "-wd", wd, "-n", name, "-Og", "-Op"};