Implemented frequencies analysis

src/frequencies.cpp

@@ -2,4 +2,73 @@
 
 void frequencies(Parameters &parameters) {
 
+    /* The frequencies function parses through a file generated by process_reads to compute the distribution of markers
+     * between individuals. The output file has the following structure:
+     * Number of individuals | Number of markers found in this number of individuals
+     */
+
+    std::string par = "input_file_path";
+    std::ifstream input_file;
+    input_file.open(parameters.get_value_from_name<std::string>(par));
+
+    par = "min_cov";
+    int min_cov = parameters.get_value_from_name<int>(par) - 1; // -1 allows comparison with > instead of >=
+
+    if (input_file) {
+
+        std::map<uint, uint> results;  // Results --> {Frequency: count}
+
+        par = "output_file_path";
+        std::ofstream output_file;
+        output_file.open(parameters.get_value_from_name<std::string>(par));
+        output_file << "Frequency" << "\t" << "Count" << "\n"; // Header of output file
+
+        // First line of input file is the header, which is not used in this analysis
+        std::string temp = "";
+        std::getline(input_file, temp);
+
+        // Define variables used to read the file
+        char buffer[65536];
+        uint k = 0, field_n = 0, count = 0;
+
+        do {
+
+            // Read a chunk of size given by the buffer
+            input_file.read(buffer, sizeof(buffer));
+            k = input_file.gcount();
+
+            for (uint i=0; i<k; ++i) {
+
+                // Read the buffer character by character
+                switch(buffer[i]) {
+
+                case '\r':
+                    break;
+                case '\t':  // New field
+                    if (field_n > 1 and std::stoi(temp) > min_cov) ++count;  // Individual fields start at 2
+                    temp = "";
+                    ++field_n;
+                    break;
+                case '\n':  // New line (also a new field)
+                    if (field_n > 1 and std::stoi(temp) > min_cov) ++count;  // Individual fields start at 2
+                    ++results[count];
+                    // Reset variables
+                    temp = "";
+                    field_n = 0;
+                    count = 0;
+                    break;
+                default:
+                    temp += buffer[i];
+                    break;
+                }
+            }
+
+        } while (input_file);
+
+        // Cannot iterate over the map normally as it
+        uint n_individuals = results.rbegin()->first + 1; // Find the maximum number of individuals
+        for (uint i=1; i < n_individuals; ++i) output_file << i << "\t" << results[i] << "\n";  // Iterate over the map
+        output_file.close();
+        input_file.close();
+    }
 }

src/frequencies.h

@@ -2,7 +2,7 @@
 #include <string>
 #include <vector>
 #include <fstream>
-#include <unordered_map>
+#include <map>
 #include "utils.h"
 #include "parameters.h"
 #include "popmap_file.h"