Sex distribution matrix now has 0 at position 0, 0

Sequences not found in any individual are an artefact of coverage filtering and are not relevant for other analyses

src/output.cpp

@@ -12,7 +12,6 @@ void output_process_reads(std::string& output_file_path, std::vector<std::string
      * - A matrix of coverage [Individual: [Sequence, Coverage]]
      */
 
-
     FILE* output_file;
     output_file = fopen(output_file_path.c_str(), "w");
 
@@ -65,6 +64,8 @@ void output_sex_distribution(std::string& output_file_path, std::unordered_map<u
 
     uint i = 0;
 
+    results[0][0] = 0; // Sequences found in none of the individuals (after filtering for minimum coverage) should not appear in the results
+
     for (uint f=0; f < n_females; ++f) {
         for (uint m=0; m < n_males; ++m) {
             output_file << results[m][f];

src/sex_distribution.cpp

@@ -9,6 +9,7 @@ void sex_distribution(Parameters& parameters) {
      */
 
     std::unordered_map<std::string, bool> popmap = load_popmap(parameters);
+
     // Find number of males and females
     uint n_males = 0, n_females = 0;
     for (auto i: popmap) if (i.second) ++n_males; else ++n_females;