Support multiple inputs

  }

  // For mapping

  Chromap(int error_threshold, int match_score, int mismatch_penalty, const std::vector<int> &gap_open_penalties, const std::vector<int> &gap_extension_penalties, int min_num_seeds_required_for_mapping, const std::vector<int> &max_seed_frequencies, int max_num_best_mappings, int max_insert_size, uint8_t mapq_threshold, int num_threads, int min_read_length, int multi_mapping_allocation_distance, int multi_mapping_allocation_seed, int drop_repetitive_reads, bool trim_adapters, bool remove_pcr_duplicates, bool is_bulk_data, bool allocate_multi_mappings, bool only_output_unique_mappings, bool Tn5_shift, bool output_mapping_in_BED, bool output_mapping_in_TagAlign, bool output_mapping_in_PAF, bool low_memory_mode, bool cell_by_bin, int bin_size, uint16_t depth_cutoff_to_call_peak, int peak_min_length, int peak_merge_max_length, const std::string &reference_file_path, const std::string &index_file_path, const std::string &read_file1_path, const std::string &read_file2_path, const std::string &barcode_file_path, const std::string &barcode_whitelist_file_path, const std::string &mapping_output_file_path, const std::string &matrix_output_prefix) : error_threshold_(error_threshold), match_score_(match_score), mismatch_penalty_(mismatch_penalty), gap_open_penalties_(gap_open_penalties), gap_extension_penalties_(gap_extension_penalties), min_num_seeds_required_for_mapping_(min_num_seeds_required_for_mapping), max_seed_frequencies_(max_seed_frequencies), max_num_best_mappings_(max_num_best_mappings), max_insert_size_(max_insert_size), mapq_threshold_(mapq_threshold), num_threads_(num_threads), min_read_length_(min_read_length), multi_mapping_allocation_distance_(multi_mapping_allocation_distance), multi_mapping_allocation_seed_(multi_mapping_allocation_seed), drop_repetitive_reads_(drop_repetitive_reads), trim_adapters_(trim_adapters), remove_pcr_duplicates_(remove_pcr_duplicates), is_bulk_data_(is_bulk_data), allocate_multi_mappings_(allocate_multi_mappings), only_output_unique_mappings_(only_output_unique_mappings), Tn5_shift_(Tn5_shift), output_mapping_in_BED_(output_mapping_in_BED), output_mapping_in_TagAlign_(output_mapping_in_TagAlign), output_mapping_in_PAF_(output_mapping_in_PAF), low_memory_mode_(low_memory_mode), cell_by_bin_(cell_by_bin), bin_size_(bin_size), depth_cutoff_to_call_peak_(depth_cutoff_to_call_peak), peak_min_length_(peak_min_length), peak_merge_max_length_(peak_merge_max_length), reference_file_path_(reference_file_path), index_file_path_(index_file_path), read_file1_path_(read_file1_path), read_file2_path_(read_file2_path), barcode_file_path_(barcode_file_path), barcode_whitelist_file_path_(barcode_whitelist_file_path), mapping_output_file_path_(mapping_output_file_path), matrix_output_prefix_(matrix_output_prefix) {

  Chromap(int error_threshold, int match_score, int mismatch_penalty, const std::vector<int> &gap_open_penalties, const std::vector<int> &gap_extension_penalties, int min_num_seeds_required_for_mapping, const std::vector<int> &max_seed_frequencies, int max_num_best_mappings, int max_insert_size, uint8_t mapq_threshold, int num_threads, int min_read_length, int multi_mapping_allocation_distance, int multi_mapping_allocation_seed, int drop_repetitive_reads, bool trim_adapters, bool remove_pcr_duplicates, bool is_bulk_data, bool allocate_multi_mappings, bool only_output_unique_mappings, bool Tn5_shift, bool output_mapping_in_BED, bool output_mapping_in_TagAlign, bool output_mapping_in_PAF, bool low_memory_mode, bool cell_by_bin, int bin_size, uint16_t depth_cutoff_to_call_peak, int peak_min_length, int peak_merge_max_length, const std::string &reference_file_path, const std::string &index_file_path, const std::vector<std::string> &read_file1_paths, const std::vector<std::string> &read_file2_paths, const std::vector<std::string> &barcode_file_paths, const std::string &barcode_whitelist_file_path, const std::string &mapping_output_file_path, const std::string &matrix_output_prefix) : error_threshold_(error_threshold), match_score_(match_score), mismatch_penalty_(mismatch_penalty), gap_open_penalties_(gap_open_penalties), gap_extension_penalties_(gap_extension_penalties), min_num_seeds_required_for_mapping_(min_num_seeds_required_for_mapping), max_seed_frequencies_(max_seed_frequencies), max_num_best_mappings_(max_num_best_mappings), max_insert_size_(max_insert_size), mapq_threshold_(mapq_threshold), num_threads_(num_threads), min_read_length_(min_read_length), multi_mapping_allocation_distance_(multi_mapping_allocation_distance), multi_mapping_allocation_seed_(multi_mapping_allocation_seed), drop_repetitive_reads_(drop_repetitive_reads), trim_adapters_(trim_adapters), remove_pcr_duplicates_(remove_pcr_duplicates), is_bulk_data_(is_bulk_data), allocate_multi_mappings_(allocate_multi_mappings), only_output_unique_mappings_(only_output_unique_mappings), Tn5_shift_(Tn5_shift), output_mapping_in_BED_(output_mapping_in_BED), output_mapping_in_TagAlign_(output_mapping_in_TagAlign), output_mapping_in_PAF_(output_mapping_in_PAF), low_memory_mode_(low_memory_mode), cell_by_bin_(cell_by_bin), bin_size_(bin_size), depth_cutoff_to_call_peak_(depth_cutoff_to_call_peak), peak_min_length_(peak_min_length), peak_merge_max_length_(peak_merge_max_length), reference_file_path_(reference_file_path), index_file_path_(index_file_path), read_file1_paths_(read_file1_paths), read_file2_paths_(read_file2_paths), barcode_file_paths_(barcode_file_paths), barcode_whitelist_file_path_(barcode_whitelist_file_path), mapping_output_file_path_(mapping_output_file_path), matrix_output_prefix_(matrix_output_prefix) {

    barcode_lookup_table_ = kh_init(k32);

    barcode_whitelist_lookup_table_ = kh_init(k32_set);

    barcode_histogram_ = kh_init(k32);

  int peak_merge_max_length_;

  std::string reference_file_path_;

  std::string index_file_path_;

  std::string read_file1_path_;

  std::string read_file2_path_;

  std::string barcode_file_path_;

  std::vector<std::string> read_file1_paths_;

  std::vector<std::string> read_file2_paths_;

  std::vector<std::string> barcode_file_paths_;

  std::string barcode_whitelist_file_path_;

  std::string mapping_output_file_path_;

  FILE *mapping_output_file_;