Major code cleanup. Rewrote CLI and parameters system entirely using CLI11.

CLI should be frozen until 1.0.0 hopefully. Setup for implementing the last changes before 1.0.0

include/cli11/LICENSE.txt

+CLI11 1.7 Copyright (c) 2017-2019 University of Cincinnati, developed by Henry
+Schreiner under NSF AWARD 1414736. All rights reserved.
+
+Redistribution and use in source and binary forms of CLI11, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software without
+   specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

makefile

 # Compiler options
 CC = g++
 OPTCFLAGS = -O2
-CFLAGS = -Wall -std=c++11 $(OPTCFLAGS)
+CFLAGS = -Wall -Wno-maybe-uninitialized -std=c++11 $(OPTCFLAGS)
 LDFLAGS = -pthread -static-libstdc++ -lz
 
 # Directory organisation

src/depth.cpp

@@ -4,9 +4,8 @@ void depth(Parameters& parameters) {
 
     std::unordered_map<std::string, bool> popmap = load_popmap(parameters);
 
-    std::string par = "input_file_path";
     std::ifstream input_file;
-    input_file.open(parameters.get_value_from_name<std::string>(par));
+    input_file.open(parameters.markers_table_path);
 
     if (input_file.is_open()) {
 
@@ -17,19 +16,7 @@ void depth(Parameters& parameters) {
         header = split(temp, "\t");
 
         // Map with column number --> index of sex_count (0 = male, 1 = female, 2 = no sex)
-        std::unordered_map<uint, uint> sex_columns;
-
-        for (uint i=0; i<header.size(); ++i) {
-            if (popmap.find(header[i]) != popmap.end()) {
-                if (popmap[header[i]]) {
-                    sex_columns[i] = 0; // Male --> column 0
-                } else {
-                    sex_columns[i] = 1; // Female --> column 1
-                }
-            } else {
-                sex_columns[i] = 2; // First and second columns (id and sequence) are counted as no sex
-            }
-        }
+        std::unordered_map<uint, uint> sex_columns = get_column_sex(popmap, line);
 
         std::unordered_map<std::string, uint> individual_depths;
 
@@ -42,29 +29,29 @@ void depth(Parameters& parameters) {
 
             // Read a chunk of size given by the buffer
             input_file.read(buffer, sizeof(buffer));
-            k = input_file.gcount();
+            k = static_cast<uint>(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 (sex_columns[field_n] != 2) individual_depths[header[field_n]] += std::stoul(temp);  // Increment the appropriate counter
-                    temp = "";
-                    ++field_n;
-                    break;
-                case '\n':  // New line (also a new field)
-                    if (sex_columns[field_n] != 2) individual_depths[header[field_n]] += std::stoul(temp);  // Increment the appropriate counter
-                    // Reset variables
-                    temp = "";
-                    field_n = 0;
-                    break;
-                default:
-                    temp += buffer[i];
-                    break;
+                    case '\t':  // New field
+                        if (sex_columns[field_n] != 2) individual_depths[header[field_n]] += std::stoul(temp);  // Increment the appropriate counter
+                        temp = "";
+                        ++field_n;
+                        break;
+
+                    case '\n':  // New line (also a new field)
+                        if (sex_columns[field_n] != 2) individual_depths[header[field_n]] += std::stoul(temp);  // Increment the appropriate counter
+                        // Reset variables
+                        temp = "";
+                        field_n = 0;
+                        break;
+
+                    default:
+                        temp += buffer[i];
+                        break;
                 }
             }
 
@@ -72,10 +59,8 @@ void depth(Parameters& parameters) {
 
         input_file.close();
 
-        par = "output_file_path";
-        std::string output_file_path = parameters.get_value_from_name<std::string>(par);
         std::ofstream output_file;
-        output_file.open(output_file_path);
+        output_file.open(parameters.output_file_path);
 
         if (output_file.is_open()) {
 

src/depth.h

 #pragma once
-#include <string>
-#include <vector>
 #include <fstream>
+#include <string>
 #include <unordered_map>
-#include "utils.h"
+#include <vector>
+#include "output.h"
 #include "parameters.h"
 #include "popmap.h"
-#include "output.h"
-
+#include "utils.h"
 
-// Main function implementing the analysis
+// Calculate the number of reads retained in each individual
 void depth(Parameters& parameters);

src/distrib.cpp

@@ -13,16 +13,9 @@ void distrib(Parameters& 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;
-    // Extra increment for easier comparison
-    ++n_males;
-    ++n_females;
 
-    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 >=
+    input_file.open(parameters.markers_table_path);
 
     if (input_file) {
 
@@ -33,19 +26,7 @@ void distrib(Parameters& parameters) {
         line = split(temp, "\t");
 
         // Map with column number --> index of sex_count (0 = male, 1 = female, 2 = no sex)
-        std::unordered_map<uint, uint> sex_columns;
-
-        for (uint i=0; i<line.size(); ++i) {
-            if (popmap.find(line[i]) != popmap.end()) {
-                if (popmap[line[i]]) {
-                    sex_columns[i] = 0; // Male --> column 0
-                } else {
-                    sex_columns[i] = 1; // Female --> column 1
-                }
-            } else {
-                sex_columns[i] = 2; // First and second columns (id and sequence) are counted as no sex
-            }
-        }
+        std::unordered_map<uint, uint> sex_columns = get_column_sex(popmap, line);
 
         // Define variables used to read the file
         char buffer[65536];
@@ -57,32 +38,32 @@ void distrib(Parameters& parameters) {
 
             // Read a chunk of size given by the buffer
             input_file.read(buffer, sizeof(buffer));
-            k = input_file.gcount();
+            k = static_cast<uint>(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 (sex_columns[field_n] != 2 and std::stoi(temp) > min_cov) ++sex_count[sex_columns[field_n]];  // Increment the appropriate counter
-                    temp = "";
-                    ++field_n;
-                    break;
-                case '\n':  // New line (also a new field)
-                    if (sex_columns[field_n] != 2 and std::stoi(temp) > min_cov) ++sex_count[sex_columns[field_n]];  // Increment the appropriate counter
-                    ++results[sex_count[0]][sex_count[1]].first; // Update the results
-                    // Reset variables
-                    temp = "";
-                    field_n = 0;
-                    sex_count[0] = 0;
-                    sex_count[1] = 0;
-                    break;
-                default:
-                    temp += buffer[i];
-                    break;
+                    case '\t':  // New field
+                        if (sex_columns[field_n] != 2 and static_cast<uint>(std::stoi(temp)) >= parameters.min_depth) ++sex_count[sex_columns[field_n]];  // Increment the appropriate counter
+                        temp = "";
+                        ++field_n;
+                        break;
+
+                    case '\n':  // New line (also a new field)
+                        if (sex_columns[field_n] != 2 and static_cast<uint>(std::stoi(temp)) >= parameters.min_depth) ++sex_count[sex_columns[field_n]];  // Increment the appropriate counter
+                        ++results[sex_count[0]][sex_count[1]].first; // Update the results
+                        // Reset variables
+                        temp = "";
+                        field_n = 0;
+                        sex_count[0] = 0;
+                        sex_count[1] = 0;
+                        break;
+
+                    default:
+                        temp += buffer[i];
+                        break;
                 }
             }
 
@@ -94,8 +75,8 @@ void distrib(Parameters& parameters) {
         double chi_squared = 0;
 
         // Compute p-values
-        for (uint f=0; f < n_females; ++f) {
-            for (uint m=0; m < n_males; ++m) {
+        for (uint f=0; f <= n_females; ++f) {
+            for (uint m=0; m <= n_males; ++m) {
                 if (f + m != 0) {
                     chi_squared = get_chi_squared(m, f, n_males, n_females);
                     results[m][f].second = std::min(1.0, get_chi_squared_p(chi_squared)); // p-value corrected with Bonferroni, with max of 1
@@ -103,17 +84,11 @@ void distrib(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
-        if (!output_matrix) {
-            output_sex_distribution(output_file_path, results, n_males, n_females);
+        if (!parameters.output_matrix) {
+            output_sex_distribution(parameters.output_file_path, results, n_males, n_females);
         } else {
-            output_sex_distribution_matrix(output_file_path, results, n_males, n_females);
+            output_sex_distribution_matrix(parameters.output_file_path, results, n_males, n_females);
         }
     }
 }

src/distrib.h

 #pragma once
-#include <string>
-#include <vector>
 #include <fstream>
+#include <string>
 #include <unordered_map>
-#include "utils.h"
+#include <vector>
+#include "output.h"
 #include "parameters.h"
 #include "popmap.h"
-#include "output.h"
-
+#include "utils.h"
 
-// Main function implementing the analysis
+// Compute the distribution of markers between males and females
 void distrib(Parameters& parameters);

src/freq.cpp

@@ -7,22 +7,13 @@ void freq(Parameters &parameters) {
      * 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 >=
+    input_file.open(parameters.markers_table_path);
 
     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);
@@ -35,36 +26,40 @@ void freq(Parameters &parameters) {
 
             // Read a chunk of size given by the buffer
             input_file.read(buffer, sizeof(buffer));
-            k = input_file.gcount();
+            k = static_cast<uint>(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;
+                    case '\t':  // New field
+                        if (field_n > 1 and static_cast<uint>(std::stoi(temp)) >= parameters.min_depth) ++count;  // Individual fields start at 2
+                        temp = "";
+                        ++field_n;
+                        break;
+
+                    case '\n':  // New line (also a new field)
+                        if (field_n > 1 and static_cast<uint>(std::stoi(temp)) >= parameters.min_depth) ++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);
 
+        std::ofstream output_file;
+        output_file.open(parameters.output_file_path);
+        output_file << "Frequency" << "\t" << "Count" << "\n"; // Header of output 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