Fixed subset not computing max number of individuals + allowed to override popmap groups with -G

src/parameters.h

@@ -32,8 +32,8 @@ struct Parameters {
     // "subset" specific parameters
     uint subset_min_group1 = 0;
     uint subset_min_group2 = 0;
-    uint subset_max_group1 = 0;
-    uint subset_max_group2 = 0;
+    uint subset_max_group1 = 9999;
+    uint subset_max_group2 = 9999;
     uint subset_min_individuals = 0;
     uint subset_max_individuals = 9999;
 

src/popmap.cpp

@@ -52,11 +52,15 @@ Popmap load_popmap(Parameters& parameters, bool compare) {
         log("Groups specified with --groups (\"" + parameters.group1 + "\", \"" + parameters.group2 + "\") were not found in popmap groups (" + print_groups(popmap) + ")", LOG_ERROR);
         exit(1);
 
-    } else if (compare and popmap.counts.size() == 2) {  // If only two groups in popmap, use them (override user-specified groups for now)
+    } else if (compare and popmap.counts.size() == 2) {  // Only two groups in popmap
 
-        auto i = std::begin(popmap.counts);
-        parameters.group1 = i->first;
-        parameters.group2 = (++i)->first;
+        if (parameters.group1 == "" and parameters.group2 == "") {  // Fill groups from popmap if not specified by the user
+
+            auto i = std::begin(popmap.counts);
+            parameters.group1 = i->first;
+            parameters.group2 = (++i)->first;
+
+        }
     }
 
     std::string popmap_success_message = "Loaded popmap (" + print_groups(popmap, true) + ")";

src/subset.cpp

@@ -6,6 +6,10 @@ void subset(Parameters& parameters) {
 
     Popmap popmap = load_popmap(parameters);
 
+    if (parameters.set_max_group1) parameters.subset_max_group1 = popmap.counts[parameters.group1];
+    if (parameters.set_max_group2) parameters.subset_max_group2 = popmap.counts[parameters.group2];
+    if (parameters.set_max_individuals) parameters.subset_max_individuals = static_cast<uint>(popmap.groups.size());
+
     log("RADSex subset started");
     log("Comparing groups \"" + parameters.group1 + "\" and \"" + parameters.group2 + "\"");
 
@@ -56,7 +60,7 @@ void processor(MarkersQueue& markers_queue, Popmap& popmap, Parameters& paramete
                     marker.n_individuals >= parameters.subset_min_individuals and marker.n_individuals <= parameters.subset_max_individuals) {
 
                     chi_squared = get_chi_squared(marker.groups[parameters.group1], marker.groups[parameters.group2], popmap.counts[parameters.group1], popmap.counts[parameters.group2]);
-                    marker.p = get_chi_squared_p(chi_squared);
+                    marker.p = static_cast<float>(get_chi_squared_p(chi_squared));
 
                     parameters.output_fasta ? marker.output_fasta(output_file, parameters.min_depth) : marker.output_table(output_file);