Fixed bug in 'map' for low number of samples

src/map.cpp

@@ -27,7 +27,7 @@
 void Map::extra_setup() {
 
     // Filtering
-    this->min_individuals = static_cast<uint16_t>(this->popmap.n_individuals * this->parameters.map_min_frequency);
+    this->min_individuals = std::max(static_cast<uint16_t>(1), static_cast<uint16_t>(this->popmap.n_individuals * this->parameters.map_min_frequency));
 
     // Loading bwa index
     this->load_bwa_index();

src/map.h

@@ -22,6 +22,7 @@
 */
 
 #pragma once
+#include <algorithm>
 #include <fstream>
 #include <string>
 #include <unordered_map>

src/markers_table.cpp

@@ -84,6 +84,7 @@ void MarkersTable::start_parser(bool store_sequence, bool compute_groups) {
     char buffer[65536];
     uint k = 0, field_n = 0, marker_n = 0;
     Marker marker(this->header.n_individuals);
+    for (auto g: this->popmap->get_groups()) marker.group_counts[g] = 0;  // Initialize group counts
     std::vector<Marker> tmp_queue(TMP_QUEUE_SIZE);  // Temporary block queue to avoid locking the shared blocks queue too often
     uint tmp_queue_real_size = 0;
     uint marker_queue_size = 0;

src/popmap.cpp

@@ -134,6 +134,17 @@ uint Popmap::get_count(const std::string& group) const {
 
 
 
+std::vector<std::string> Popmap::get_groups() const {
+
+    std::vector<std::string> groups;
+    for (auto g: this->group_counts) groups.push_back(g.first);
+
+    return groups;
+
+}
+
+
+
 
 std::string Popmap::print_groups(const bool counts) const {
 

src/popmap.h

@@ -80,6 +80,15 @@ class Popmap {
         uint get_count(const std::string& group) const;
 
 
+        /*!
+         * \brief Get a list of all groups found in the popmap
+         *
+         * \return A vector of group names
+         */
+
+        std::vector<std::string> get_groups() const;
+
+
         /*!
          * \brief Print all the groups in the popmap
          *