read sequence from ifstream into string

src/aevol_create.cpp

@@ -40,7 +40,9 @@ const char* DEFAULT_PARAM_FILE_NAME = "param.in";
 
 #include <getopt.h>
 
+#include <fstream>
 #include <sstream>
+#include <string>
 
 #include "legacy/ExpManager.h"
 #include "aevol_version.h"
@@ -70,35 +72,28 @@ int main(int argc, char* argv[]) {
   // Initialize the experiment manager
   exp_manager = new ExpManager();
 
-
   // Initialize the simulation from the parameter file
-  int32_t lchromosome = -1;
-  char* chromosome = nullptr;
+  std::string chromosome;
 
   if (chromosome_file_name != nullptr) {
-    const int max_input_chrom_size = 1000000;
-    char raw_chromosome[max_input_chrom_size];
-    FILE* chromosome_file = fopen(chromosome_file_name, "r");
-    if (chromosome_file == nullptr) {
+    std::ifstream chromosome_file(chromosome_file_name);
+    if (not chromosome_file) {
       Utils::ExitWithUsrMsg(std::string("failed to open source chromosome file ") + chromosome_file_name);
     }
-    if (fgets(raw_chromosome, max_input_chrom_size, chromosome_file) == nullptr)
-    {
+
+    std::getline(chromosome_file, chromosome);
+    if (not chromosome_file or chromosome.length() == 0) {
       Utils::ExitWithUsrMsg(std::string("failed to read from chromosome file ") + chromosome_file_name);
     }
-    lchromosome = strlen(raw_chromosome) - 1;
-    chromosome = new char[lchromosome + 1];
-    strncpy(chromosome, raw_chromosome, lchromosome + 1);
-    printf("Loading chromosome from text file %s (%" PRId32 " base pairs) \n",
-        chromosome_file_name, lchromosome);
+
+    std::cout << "Loading chromosome from text file " << chromosome_file_name << " (" << chromosome.length()
+              << " base pairs)" << std::endl;
     delete [] chromosome_file_name;
-    fclose(chromosome_file);
   }
 
   if(param_file_name != nullptr) {
-    if (lchromosome > -1) {
-      ParamLoader::load(param_values, exp_manager, true, chromosome, lchromosome);
-      delete chromosome;
+    if (chromosome.length() != 0) {
+      ParamLoader::load(param_values, exp_manager, true, chromosome.c_str(), chromosome.length());
     } else {
       ParamLoader::load(param_values, exp_manager, true);
     }