Add missing shared variables in omp region.

      }

    }

#pragma omp parallel default(none) shared(output_mappings_not_in_whitelist_, barcode_whitelist_file_path_, trim_adapters_, window_size_, custom_rid_order_path_, split_alignment_, error_threshold_, max_num_best_mappings_, num_threads_, num_reads_, low_memory_mode_, num_reference_sequences, reference, index, read_batch1, read_batch2, barcode_batch, read_batch1_for_loading, read_batch2_for_loading, barcode_batch_for_loading, candidate_processor, output_tools_, std::cerr, num_loaded_pairs_for_loading, num_loaded_pairs, mappings_on_diff_ref_seqs_for_diff_threads, mappings_on_diff_ref_seqs_for_diff_threads_for_saving, mappings_on_diff_ref_seqs_, mapping_output_file_path_, num_mappings_in_mem, max_num_mappings_in_mem, temp_mapping_file_handles_, mm_to_candidates_cache, mm_history1, mm_history2) num_threads(num_threads_) reduction(+:num_candidates_, num_mappings_, num_mapped_reads_, num_uniquely_mapped_reads_, num_barcode_in_whitelist_, num_corrected_barcode_)

#pragma omp parallel default(none) shared(output_mappings_not_in_whitelist_, barcode_whitelist_file_path_, trim_adapters_, window_size_, custom_rid_order_path_, split_alignment_, error_threshold_, max_seed_frequencies_, max_num_best_mappings_, max_insert_size_, num_threads_, num_reads_, low_memory_mode_, num_reference_sequences, reference, index, read_batch1, read_batch2, barcode_batch, read_batch1_for_loading, read_batch2_for_loading, barcode_batch_for_loading, candidate_processor, output_tools_, std::cerr, num_loaded_pairs_for_loading, num_loaded_pairs, mappings_on_diff_ref_seqs_for_diff_threads, mappings_on_diff_ref_seqs_for_diff_threads_for_saving, mappings_on_diff_ref_seqs_, mapping_output_file_path_, num_mappings_in_mem, max_num_mappings_in_mem, temp_mapping_file_handles_, mm_to_candidates_cache, mm_history1, mm_history2) num_threads(num_threads_) reduction(+:num_candidates_, num_mappings_, num_mapped_reads_, num_uniquely_mapped_reads_, num_barcode_in_whitelist_, num_corrected_barcode_)

    {

      thread_num_candidates = 0;

      thread_num_mappings = 0;

            num_threads_ / num_reference_sequences);

      }

    }

#pragma omp parallel default(none) shared(window_size_, custom_rid_order_path_, error_threshold_, max_num_best_mappings_, num_threads_, num_reads_, mm_history, reference, index, read_batch, barcode_batch, read_batch_for_loading, barcode_batch_for_loading, std::cerr, num_loaded_reads_for_loading, num_loaded_reads, num_reference_sequences, mappings_on_diff_ref_seqs_for_diff_threads, mappings_on_diff_ref_seqs_for_diff_threads_for_saving, mm_to_candidates_cache, output_tools_, candidate_processor) num_threads(num_threads_) reduction(+:num_candidates_, num_mappings_, num_mapped_reads_, num_uniquely_mapped_reads_, num_barcode_in_whitelist_, num_corrected_barcode_)

#pragma omp parallel default(none) shared(barcode_whitelist_file_path_, output_mappings_not_in_whitelist_, window_size_, custom_rid_order_path_, error_threshold_, max_num_best_mappings_, max_seed_frequencies_, num_threads_, num_reads_, mm_history, reference, index, read_batch, barcode_batch, read_batch_for_loading, barcode_batch_for_loading, std::cerr, num_loaded_reads_for_loading, num_loaded_reads, num_reference_sequences, mappings_on_diff_ref_seqs_for_diff_threads, mappings_on_diff_ref_seqs_for_diff_threads_for_saving, mm_to_candidates_cache, output_tools_, candidate_processor) num_threads(num_threads_) reduction(+:num_candidates_, num_mappings_, num_mapped_reads_, num_uniquely_mapped_reads_, num_barcode_in_whitelist_, num_corrected_barcode_)

    {

      thread_num_candidates = 0;

      thread_num_mappings = 0;