WIP.

include/generation_rs.h

@@ -320,7 +320,7 @@ struct population_marker_observation {
     marker_data observations;
 
     std::map<char, VectorXb> observation_vectors;
-    
+
     void compute_observation_vectors(
             const impl::generation_rs* g,
             const marker_observation_spec& obs_spec);

include/settings.h

@@ -37,6 +37,8 @@ struct settings_t {
     std::string map_filename;
     std::vector<chromosome> map;
     /*format_specification_t* marker_observation_specs;*/
+    enum observation_type_t { Geno, Line };
+    observation_type_t observation_type;
     std::map<std::string, marker_observation_spec> marker_observation_specs;
     std::vector<std::string> marker_observation_specs_filenames;
     std::map<std::string, population> populations;
@@ -98,6 +100,7 @@ struct settings_t {
         : notes()
         , design(0)
         , map_filename(), map()
+        , observation_type(ObsLine)
         , marker_observation_specs()
         , populations()
         , working_set()
@@ -264,6 +267,20 @@ struct format_specification_t {
 };
 
 
+inline std::ostream& operator << (std::ostream& os, settings_t::observation_type_t ot)
+{
+    switch (ot) {
+        case settings_t::observation_type_t::Line:
+            os << "line";
+            break;
+        case settings_t::observation_type_t::Geno:
+            os << "geno";
+            break;
+    };
+    return os;
+}
+
+
 std::ostream& operator << (std::ostream&, const settings_t&);
 
 namespace read_data {

src/input/read_settings.cc

@@ -7,7 +7,7 @@
 #include "labelled_matrix.h"
 #include "cache2.h"
 #include "model.h"
-#include "computations/basic_data.h"
+#include "computations/probabilities.h"
 
 #include <regex>
 
@@ -416,6 +416,47 @@ arguments = {
                 exit(0);
                 SAFE_IGNORE_CALLBACK_ARGS;
             }},
+        {{"-Dpop", "--dump-POP"},
+            {},
+            "[DEBUG] Dump parental origin probabilities and exit",
+            true,
+            {},
+            [](CALLBACK_ARGS)
+            {
+                ensure(target);
+                active_settings = target;
+
+                msg_handler_t::check(true);
+                active_settings->finalize();
+                active_settings->set_title("Checking the validity of the configuration");
+                if (!active_settings->sanity_check()) {
+                    exit(-1);
+                }
+                msg_handler_t::check(true);
+                locus_key lk;
+                Eigen::IOFormat fmt(StreamPrecision, DontAlignCols, "\t", "\n", "", "", "", "");
+                for (const chromosome& c: active_settings->map) {
+                    auto loci = compute_steps(c.condensed.marker_locus, target->step);
+                    for (const auto& kv: active_settings->populations) {
+                        const auto& pop = kv.second;
+                        context_key ck(new context_key_struc(&pop, &c, loci));
+                        auto vck = as_value(ck);
+                        collection<multi_generation_observations>
+                            vmgo = make_collection<Disk>(population_marker_obs,
+                                                         vck, range<int>(0, ck->pop->size(), 1));
+                        collection<locus_probabilities_type>
+                            alp = make_collection<Disk>(locus_probabilities,
+                                    vck, as_value(lk), vmgo, as_value(ck->loci));
+                        OUT("CHROMOSOME " << c.name << " POPULATION " << kv.first << std::endl);
+                        int i = 0;
+                        for (const auto& pm: alp) {
+                            OUT('#' << (++i) << std::endl << pm << std::endl);
+                        }
+                    }
+                }
+                exit(0);
+                SAFE_IGNORE_CALLBACK_ARGS;
+            }},
         {{"-Dstfopom", "--dump-stfopom"},
             {"gen", "order"},
             "[DEBUG] Dump ST(fo)POM",
@@ -648,6 +689,17 @@ arguments = {
                 SAFE_IGNORE_CALLBACK_ARGS;
             }},
 
+        {{"-ot", "--observation-type"},
+            {"type"},
+            "Specify how to interpret the observation data.\nIf type is 'line'" /* TODO */,
+            false,
+            {&settings_t::observation_type},
+            [](CALLBACK_ARGS)
+            {
+                /* TODO */
+                SAFE_IGNORE_CALLBACK_ARGS;
+            }},
+
         {{"-mos", "--marker-observations-spec"},
             {"path"},
             "Path to the marker observation specification file",