BUG: Fix 0-record bam file error

src/bam_module.cpp

@@ -32,20 +32,41 @@ int BAM_Module::calculateStatistics(Input_Para& input_params, Output_BAM& final_
  HTSReader reader(filepath);
  std::cout<<"Processing file: "<< filepath << std::endl;
 
- // Get the number of threads
+ // Get the number of threads (Set to 1 if the number of threads is not specified/invalid)
  int thread_count = input_params.threads;
+ if (thread_count < 1) {
+ thread_count = 1;
+ }
 
  // Get the number of records in the file using the BAM index
  std::cout << "Getting number of records..." << std::endl;
  int num_records = reader.getNumRecords(filepath);
  std::cout << "Number of records = " << num_records << std::endl;
 
+ // Exit if there are no records
+ if (num_records == 0){
+ std::cerr << "No records found in file: " << filepath << std::endl;
+ exit_code = 1;
+ return exit_code;
+ }
+
  // Determine the batch size if the thread count is greater than 1
  int batch_size = 0;
  if (thread_count > 1) {
- // Determine the number of records per thread
- batch_size = (int) ceil((double)num_records / (double)thread_count);
- std::cout << "Batch size (records per thread) = " << batch_size << std::endl;
+ // If the number of records is less than the number of threads, set the number of threads to the number of records
+ if (num_records < thread_count){
+ thread_count = num_records;
+ batch_size = 1;
+ std::cout << "Number of threads set to " << thread_count << std::endl;
+ std::cout << "Batch size (records per thread) = " << batch_size << std::endl;
+
+ // Otherwise, the batch size is the number of records divided by the number of threads
+ } else {
+ // Determine the number of records per thread
+ batch_size = (int) ceil((double)num_records / (double)thread_count);
+ std::cout << "Batch size (records per thread) = " << batch_size << std::endl;
+ }
+
  } else {
  // Set the batch size to the number of records
  batch_size = num_records;