Finished implementing new output + added parameter to output in old format

src/output.cpp

@@ -91,7 +91,7 @@ void output_sex_distribution(std::string& output_file_path, sd_table& results, u
     output_file.open(output_file_path);
 
     // Output file header
-    output_file << "Males" << "\t" << "Females" << "\t" << "Sequences" << "\t" << "P-value" << "\t" << "Significant" << "\n";
+    output_file << "Males" << "\t" << "Females" << "\t" << "Sequences" << "\t" << "P-value" << "\n";
 
     // Generate output file
     for (uint m=0; m < n_males; ++m) {

src/parameters.h

@@ -14,7 +14,8 @@ struct Parameters {
 
     // Initialize all possible parameters to be used in the analyses
     // Arguments: name, help message, flag, default value, type, internal type, value, required
-    // Flags : -h, -f, -d, -o, -u, -t, -c, -p, -b, -a, -m, --min-males, --min-females, --max-males, --max-females, --min-individuals
+    // Flags : -h, -f, -d, -o, -u, -t, -c, -p, -b, -a, -m, --min-males, --min-females, --max-males, --max-females, --min-individuals, --output-matrix
+    // Parameter constructor: Parameter(name, description, flag, default_value, type, internal_type, value, required)
     std::vector<Parameter> list {Parameter("help", "Prints this message", "-h", "0", "bool", "bool", "", false),
                                  Parameter("input_file_path", "Path to an input file", "-f", "", "string", "ifile", "", true),
                                  Parameter("input_dir_path", "Path to an input directory", "-d", "", "string", "dir", "", true),
@@ -32,6 +33,7 @@ struct Parameters {
                                  Parameter("max_females", "Maximum number of females in the subset", "--max-females", "n.females", "int", "int", "", false),
                                  Parameter("min_individuals", "Minimum number of individuals in the subset (overrides sex parameters)", "--min-individuals", "0", "int", "int", "", false),
                                  Parameter("max_individuals", "Maxmimum number of individuals in the subset (overrides sex parameters)", "--max-individuals", "n.individual", "int", "int", "", false),
+                                 Parameter("output_matrix", "Output the sex distribution table as a matrix", "--output-matrix", "0", "bool", "bool", "", false)
                                  };
 
 

src/radsex.h

@@ -24,6 +24,7 @@ class RadSex {
         Parameters parameters;
 
         // Define all analyses
+        // Analysis constructor: Analysis(name, description, parameters, function ref)
         std::map<std::string, Analysis> analyses { {"sex_distribution",
                                                     Analysis("sex_distribution",
                                                              "Compute a matrix of sequences distribution between sexes",

src/sex_distribution.cpp

@@ -114,7 +114,14 @@ void sex_distribution(Parameters& parameters) {
         par = "output_file_path";
         std::string output_file_path = parameters.get_value_from_name<std::string>(par);
 
+        par = "output_matrix";
+        bool output_matrix = parameters.get_value_from_name<bool>(par);
+
         // Generate the output file
-        output_sex_distribution(output_file_path, results, n_males, n_females);
+        if (!output_matrix) {
+            output_sex_distribution(output_file_path, results, n_males, n_females);
+        } else {
+            output_sex_distribution_matrix(output_file_path, results, n_males, n_females);
+        }
     }
 }