repair bio input

README.md

@@ -53,10 +53,10 @@ This utility has the form `./minaa.exe <G> <H> [-B=bio] [-a=alpha] [-b=beta]`.
   - Default: the algorithm will run using only topological calculations.
 - **-a=**: alpha; the GDV-edge weight balancer.
   - Require: a real number in range [0, 1].
-  - Default: 1
+  - Default: 1 (100% GDV data).
 - **-b=**: beta; the topological-biological cost matrix balancer.
   - Require: a real number in range [0, 1].
-  - Default: 1
+  - Default: 1 (100% topological data).
 
 #### Uncommon
 

src/file_io.cpp

@@ -418,16 +418,30 @@ namespace FileIO
             throw std::runtime_error("Unable to open file " + filepath);
         }
 
-        // Parse the file directly into a matrix
+        // Parse the file directly into a matrix, skipping the first row and column
         std::vector<std::vector<double>> matrix;
         std::string line;
+        auto first_row = true;
         while (std::getline(fin, line))
         {
+            if (first_row)
+            {
+                first_row = false;
+                continue;
+            }
+
             std::stringstream ss(line);
             std::string cell;
             std::vector<double> row;
+            auto first_col = true;
             while (std::getline(ss, cell, delim))
             {
+                if (first_col)
+                {
+                    first_col = false;
+                    continue;
+                }
+
                 try
                 {
                     row.push_back(std::stod(cell));

src/util.cpp

@@ -170,10 +170,10 @@ namespace Util
     std::vector<std::vector<unsigned>> binarify(std::vector<std::vector<double>> double_matrix)
     {
         std::vector<std::vector<unsigned>> binary_matrix;
-        for (unsigned i = 1; i < double_matrix.size(); ++i)
+        for (unsigned i = 0; i < double_matrix.size(); ++i)
         {
             std::vector<unsigned> row;
-            for (unsigned j = 1; j < double_matrix[i].size(); ++j)
+            for (unsigned j = 0; j < double_matrix[i].size(); ++j)
             {
                 if (double_matrix[i][j] != 0)
                 {