Support barcode filtering by whitelist (ff50bd20) · Commits · github_fork / Chromap

src/chromap.cc

+232 −220

Original line number	Diff line number	Diff line
		@@ -123,13 +123,14 @@ bool Chromap<MappingRecord>::PairedEndReadWithBarcodeIsDuplicate(uint32_t pair_i
		}

		template <typename MappingRecord>
		void Chromap<MappingRecord>::CorrectBarcodeAt(uint32_t barcode_index, SequenceBatch barcode_batch, uint64_t num_barcode_in_whitelist, uint64_t *num_corrected_barcode) {
		bool Chromap<MappingRecord>::CorrectBarcodeAt(uint32_t barcode_index, SequenceBatch barcode_batch, uint64_t num_barcode_in_whitelist, uint64_t *num_corrected_barcode) {
		uint32_t barcode_length = barcode_batch->GetSequenceLengthAt(barcode_index);
		uint32_t barcode_key = barcode_batch->GenerateSeedFromSequenceAt(barcode_index, 0, barcode_length);
		khiter_t barcode_whitelist_lookup_table_iterator = kh_get(k32, barcode_whitelist_lookup_table_, barcode_key);
		if (barcode_whitelist_lookup_table_iterator != kh_end(barcode_whitelist_lookup_table_)) {
		// Correct barcode
		++(*num_barcode_in_whitelist);
		return true;
		} else {
		// Need to correct this barcode
		//const char *barcode = barcode_batch->GetSequenceAt(barcode_index);
		@@ -164,6 +165,7 @@ void Chromap<MappingRecord>::CorrectBarcodeAt(uint32_t barcode_index, SequenceBa
		size_t num_possible_corrected_barcodes = corrected_barcodes_with_quals.size();
		if (num_possible_corrected_barcodes == 0) {
		// Barcode cannot be corrected, leave it for downstream
		return false;
		} else if (num_possible_corrected_barcodes == 1) {
		// Just correct it
		//std::cerr << "Corrected the barcode from " << barcode << " to ";
		@@ -171,6 +173,7 @@ void Chromap<MappingRecord>::CorrectBarcodeAt(uint32_t barcode_index, SequenceBa
		//std::cerr << "score: " << corrected_barcodes_with_quals[0].score << "\n";
		++(*num_corrected_barcode);
		//std::cerr << barcode << "\n";
		return true;
		} else {
		// Select the best correction
		std::sort(corrected_barcodes_with_quals.begin(), corrected_barcodes_with_quals.end(), std::greater<BarcodeWithQual>());
		@@ -196,6 +199,7 @@ void Chromap<MappingRecord>::CorrectBarcodeAt(uint32_t barcode_index, SequenceBa
		++(*num_corrected_barcode);
		}
		//std::cerr << barcode << "\n";
		return true;
		}
		}
		}
		@@ -1039,15 +1043,17 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		#pragma omp taskloop grainsize(grain_size) //num_tasks(num_threads_* 50)
		//#pragma omp taskloop num_tasks(num_threads_* num_threads_)
		for (uint32_t pair_index = 0; pair_index < num_loaded_pairs; ++pair_index) {
		bool current_barcode_is_whitelisted = true;
		if (!barcode_whitelist_file_path_.empty()) {
		current_barcode_is_whitelisted = CorrectBarcodeAt(pair_index, &barcode_batch, &thread_num_barcode_in_whitelist, &thread_num_corrected_barcode);
		}
		if (current_barcode_is_whitelisted \|\| output_mappings_not_in_whitelist_) {
		read_batch1.PrepareNegativeSequenceAt(pair_index);
		read_batch2.PrepareNegativeSequenceAt(pair_index);
		//std::cerr << pair_index<<" "<<read_batch1.GetSequenceNameAt(pair_index) << "\n";
		if (trim_adapters_) {
		TrimAdapterForPairedEndRead(pair_index, &read_batch1, &read_batch2);
		}
		if (!barcode_whitelist_file_path_.empty()) {
		CorrectBarcodeAt(pair_index, &barcode_batch, &thread_num_barcode_in_whitelist, &thread_num_corrected_barcode);
		}
		minimizers1.clear();
		minimizers2.clear();
		minimizers1.reserve(read_batch1.GetSequenceLengthAt(pair_index) / window_size_ * 2);
		@@ -1248,6 +1254,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		}
		} // verify candidate
		}
		}
		} // for pair_index
		//if (num_reads_ / 2 > initial_num_sample_barcodes_) {
		// if (!is_bulk_data_) {
		@@ -4122,6 +4129,7 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		options.add_options("Output")
		("o,output", "Output file", cxxopts::value<std::string>(), "FILE")
		//("p,matrix-output-prefix", "Prefix of matrix output files", cxxopts::value<std::string>(), "FILE")
		("output-mappings-not-in-whitelist", "Output mappings with barcode not in the whitelist")
		("chr-order", "custom chromsome order", cxxopts::value<std::string>(), "FILE")
		("BED", "Output mappings in BED/BEDPE format")
		("TagAlign", "Output mappings in TagAlign/PairedTagAlign format")
		@@ -4167,6 +4175,7 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		bool remove_pcr_duplicates = false;
		bool remove_pcr_duplicates_at_bulk_level = true;
		bool only_output_unique_mappings = true;
		bool output_mappings_not_in_whitelist = false;
		bool allocate_multi_mappings = false;
		bool Tn5_shift = false;
		bool split_alignment = false;
		@@ -4288,6 +4297,9 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		if (result.count("split-alignment")) {
		split_alignment = true;
		}
		if (result.count("output-mappings-not-in-whitelist")) {
		output_mappings_not_in_whitelist = true;
		}
		if (result.count("BED")) {
		output_mapping_in_BED = true;
		output_mapping_in_SAM = false;
		@@ -4510,36 +4522,36 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		}
		if (result.count("2") == 0) {
		if (output_mapping_in_PAF) {
		chromap::Chromap<chromap::PAFMapping> chromap_for_mapping(error_threshold, match_score, mismatch_penalty, gap_open_penalties, gap_extension_penalties, min_num_seeds_required_for_mapping, max_seed_frequencies, max_num_best_mappings, max_insert_size, mapq_threshold, num_threads, min_read_length, multi_mapping_allocation_distance, multi_mapping_allocation_seed, drop_repetitive_reads, trim_adapters, remove_pcr_duplicates, remove_pcr_duplicates_at_bulk_level, is_bulk_data, allocate_multi_mappings, only_output_unique_mappings, Tn5_shift, split_alignment, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, output_mapping_in_SAM, output_mapping_in_pairs, low_memory_mode, cell_by_bin, bin_size, depth_cutoff_to_call_peak, peak_min_length, peak_merge_max_length, reference_file_path, index_file_path, read_file1_paths, read_file2_paths, barcode_file_paths, barcode_whitelist_file_path, output_file_path, matrix_output_prefix, custom_rid_order_path, pairs_custom_rid_order_path);
		chromap::Chromap<chromap::PAFMapping> chromap_for_mapping(error_threshold, match_score, mismatch_penalty, gap_open_penalties, gap_extension_penalties, min_num_seeds_required_for_mapping, max_seed_frequencies, max_num_best_mappings, max_insert_size, mapq_threshold, num_threads, min_read_length, multi_mapping_allocation_distance, multi_mapping_allocation_seed, drop_repetitive_reads, trim_adapters, remove_pcr_duplicates, remove_pcr_duplicates_at_bulk_level, is_bulk_data, allocate_multi_mappings, only_output_unique_mappings, output_mappings_not_in_whitelist, Tn5_shift, split_alignment, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, output_mapping_in_SAM, output_mapping_in_pairs, low_memory_mode, cell_by_bin, bin_size, depth_cutoff_to_call_peak, peak_min_length, peak_merge_max_length, reference_file_path, index_file_path, read_file1_paths, read_file2_paths, barcode_file_paths, barcode_whitelist_file_path, output_file_path, matrix_output_prefix, custom_rid_order_path, pairs_custom_rid_order_path);
		chromap_for_mapping.MapSingleEndReads();
		} else if (output_mapping_in_SAM) {
		chromap::Chromap<chromap::SAMMapping> chromap_for_mapping(error_threshold, match_score, mismatch_penalty, gap_open_penalties, gap_extension_penalties, min_num_seeds_required_for_mapping, max_seed_frequencies, max_num_best_mappings, max_insert_size, mapq_threshold, num_threads, min_read_length, multi_mapping_allocation_distance, multi_mapping_allocation_seed, drop_repetitive_reads, trim_adapters, remove_pcr_duplicates, remove_pcr_duplicates_at_bulk_level, is_bulk_data, allocate_multi_mappings, only_output_unique_mappings, Tn5_shift, split_alignment, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, output_mapping_in_SAM, output_mapping_in_pairs, low_memory_mode, cell_by_bin, bin_size, depth_cutoff_to_call_peak, peak_min_length, peak_merge_max_length, reference_file_path, index_file_path, read_file1_paths, read_file2_paths, barcode_file_paths, barcode_whitelist_file_path, output_file_path, matrix_output_prefix, custom_rid_order_path, pairs_custom_rid_order_path);
		chromap::Chromap<chromap::SAMMapping> chromap_for_mapping(error_threshold, match_score, mismatch_penalty, gap_open_penalties, gap_extension_penalties, min_num_seeds_required_for_mapping, max_seed_frequencies, max_num_best_mappings, max_insert_size, mapq_threshold, num_threads, min_read_length, multi_mapping_allocation_distance, multi_mapping_allocation_seed, drop_repetitive_reads, trim_adapters, remove_pcr_duplicates, remove_pcr_duplicates_at_bulk_level, is_bulk_data, allocate_multi_mappings, only_output_unique_mappings, output_mappings_not_in_whitelist, Tn5_shift, split_alignment, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, output_mapping_in_SAM, output_mapping_in_pairs, low_memory_mode, cell_by_bin, bin_size, depth_cutoff_to_call_peak, peak_min_length, peak_merge_max_length, reference_file_path, index_file_path, read_file1_paths, read_file2_paths, barcode_file_paths, barcode_whitelist_file_path, output_file_path, matrix_output_prefix, custom_rid_order_path, pairs_custom_rid_order_path);
		chromap_for_mapping.MapSingleEndReads();
		} else {
		if (result.count("b") != 0) {
		chromap::Chromap<chromap::MappingWithBarcode> chromap_for_mapping(error_threshold, match_score, mismatch_penalty, gap_open_penalties, gap_extension_penalties, min_num_seeds_required_for_mapping, max_seed_frequencies, max_num_best_mappings, max_insert_size, mapq_threshold, num_threads, min_read_length, multi_mapping_allocation_distance, multi_mapping_allocation_seed, drop_repetitive_reads, trim_adapters, remove_pcr_duplicates, remove_pcr_duplicates_at_bulk_level, is_bulk_data, allocate_multi_mappings, only_output_unique_mappings, Tn5_shift, split_alignment, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, output_mapping_in_SAM, output_mapping_in_pairs, low_memory_mode, cell_by_bin, bin_size, depth_cutoff_to_call_peak, peak_min_length, peak_merge_max_length, reference_file_path, index_file_path, read_file1_paths, read_file2_paths, barcode_file_paths, barcode_whitelist_file_path, output_file_path, matrix_output_prefix, custom_rid_order_path, pairs_custom_rid_order_path);
		chromap::Chromap<chromap::MappingWithBarcode> chromap_for_mapping(error_threshold, match_score, mismatch_penalty, gap_open_penalties, gap_extension_penalties, min_num_seeds_required_for_mapping, max_seed_frequencies, max_num_best_mappings, max_insert_size, mapq_threshold, num_threads, min_read_length, multi_mapping_allocation_distance, multi_mapping_allocation_seed, drop_repetitive_reads, trim_adapters, remove_pcr_duplicates, remove_pcr_duplicates_at_bulk_level, is_bulk_data, allocate_multi_mappings, only_output_unique_mappings, output_mappings_not_in_whitelist, Tn5_shift, split_alignment, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, output_mapping_in_SAM, output_mapping_in_pairs, low_memory_mode, cell_by_bin, bin_size, depth_cutoff_to_call_peak, peak_min_length, peak_merge_max_length, reference_file_path, index_file_path, read_file1_paths, read_file2_paths, barcode_file_paths, barcode_whitelist_file_path, output_file_path, matrix_output_prefix, custom_rid_order_path, pairs_custom_rid_order_path);
		chromap_for_mapping.MapSingleEndReads();
		} else {
		chromap::Chromap<chromap::MappingWithoutBarcode> chromap_for_mapping(error_threshold, match_score, mismatch_penalty, gap_open_penalties, gap_extension_penalties, min_num_seeds_required_for_mapping, max_seed_frequencies, max_num_best_mappings, max_insert_size, mapq_threshold, num_threads, min_read_length, multi_mapping_allocation_distance, multi_mapping_allocation_seed, drop_repetitive_reads, trim_adapters, remove_pcr_duplicates, remove_pcr_duplicates_at_bulk_level, is_bulk_data, allocate_multi_mappings, only_output_unique_mappings, Tn5_shift, split_alignment, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, output_mapping_in_SAM, output_mapping_in_pairs, low_memory_mode, cell_by_bin, bin_size, depth_cutoff_to_call_peak, peak_min_length, peak_merge_max_length, reference_file_path, index_file_path, read_file1_paths, read_file2_paths, barcode_file_paths, barcode_whitelist_file_path, output_file_path, matrix_output_prefix, custom_rid_order_path, pairs_custom_rid_order_path);
		chromap::Chromap<chromap::MappingWithoutBarcode> chromap_for_mapping(error_threshold, match_score, mismatch_penalty, gap_open_penalties, gap_extension_penalties, min_num_seeds_required_for_mapping, max_seed_frequencies, max_num_best_mappings, max_insert_size, mapq_threshold, num_threads, min_read_length, multi_mapping_allocation_distance, multi_mapping_allocation_seed, drop_repetitive_reads, trim_adapters, remove_pcr_duplicates, remove_pcr_duplicates_at_bulk_level, is_bulk_data, allocate_multi_mappings, only_output_unique_mappings, output_mappings_not_in_whitelist, Tn5_shift, split_alignment, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, output_mapping_in_SAM, output_mapping_in_pairs, low_memory_mode, cell_by_bin, bin_size, depth_cutoff_to_call_peak, peak_min_length, peak_merge_max_length, reference_file_path, index_file_path, read_file1_paths, read_file2_paths, barcode_file_paths, barcode_whitelist_file_path, output_file_path, matrix_output_prefix, custom_rid_order_path, pairs_custom_rid_order_path);
		chromap_for_mapping.MapSingleEndReads();
		}
		}
		} else {
		if (output_mapping_in_PAF) {
		chromap::Chromap<chromap::PairedPAFMapping> chromap_for_mapping(error_threshold, match_score, mismatch_penalty, gap_open_penalties, gap_extension_penalties, min_num_seeds_required_for_mapping, max_seed_frequencies, max_num_best_mappings, max_insert_size, mapq_threshold, num_threads, min_read_length, multi_mapping_allocation_distance, multi_mapping_allocation_seed, drop_repetitive_reads, trim_adapters, remove_pcr_duplicates, remove_pcr_duplicates_at_bulk_level, is_bulk_data, allocate_multi_mappings, only_output_unique_mappings, Tn5_shift, split_alignment, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, output_mapping_in_SAM, output_mapping_in_pairs, low_memory_mode, cell_by_bin, bin_size, depth_cutoff_to_call_peak, peak_min_length, peak_merge_max_length, reference_file_path, index_file_path, read_file1_paths, read_file2_paths, barcode_file_paths, barcode_whitelist_file_path, output_file_path, matrix_output_prefix, custom_rid_order_path, pairs_custom_rid_order_path);
		chromap::Chromap<chromap::PairedPAFMapping> chromap_for_mapping(error_threshold, match_score, mismatch_penalty, gap_open_penalties, gap_extension_penalties, min_num_seeds_required_for_mapping, max_seed_frequencies, max_num_best_mappings, max_insert_size, mapq_threshold, num_threads, min_read_length, multi_mapping_allocation_distance, multi_mapping_allocation_seed, drop_repetitive_reads, trim_adapters, remove_pcr_duplicates, remove_pcr_duplicates_at_bulk_level, is_bulk_data, allocate_multi_mappings, only_output_unique_mappings, output_mappings_not_in_whitelist, Tn5_shift, split_alignment, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, output_mapping_in_SAM, output_mapping_in_pairs, low_memory_mode, cell_by_bin, bin_size, depth_cutoff_to_call_peak, peak_min_length, peak_merge_max_length, reference_file_path, index_file_path, read_file1_paths, read_file2_paths, barcode_file_paths, barcode_whitelist_file_path, output_file_path, matrix_output_prefix, custom_rid_order_path, pairs_custom_rid_order_path);
		chromap_for_mapping.MapPairedEndReads();
		} else if (output_mapping_in_SAM) {
		chromap::Chromap<chromap::SAMMapping> chromap_for_mapping(error_threshold, match_score, mismatch_penalty, gap_open_penalties, gap_extension_penalties, min_num_seeds_required_for_mapping, max_seed_frequencies, max_num_best_mappings, max_insert_size, mapq_threshold, num_threads, min_read_length, multi_mapping_allocation_distance, multi_mapping_allocation_seed, drop_repetitive_reads, trim_adapters, remove_pcr_duplicates, remove_pcr_duplicates_at_bulk_level, is_bulk_data, allocate_multi_mappings, only_output_unique_mappings, Tn5_shift, split_alignment, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, output_mapping_in_SAM, output_mapping_in_pairs, low_memory_mode, cell_by_bin, bin_size, depth_cutoff_to_call_peak, peak_min_length, peak_merge_max_length, reference_file_path, index_file_path, read_file1_paths, read_file2_paths, barcode_file_paths, barcode_whitelist_file_path, output_file_path, matrix_output_prefix, custom_rid_order_path, pairs_custom_rid_order_path);
		chromap::Chromap<chromap::SAMMapping> chromap_for_mapping(error_threshold, match_score, mismatch_penalty, gap_open_penalties, gap_extension_penalties, min_num_seeds_required_for_mapping, max_seed_frequencies, max_num_best_mappings, max_insert_size, mapq_threshold, num_threads, min_read_length, multi_mapping_allocation_distance, multi_mapping_allocation_seed, drop_repetitive_reads, trim_adapters, remove_pcr_duplicates, remove_pcr_duplicates_at_bulk_level, is_bulk_data, allocate_multi_mappings, only_output_unique_mappings, output_mappings_not_in_whitelist, Tn5_shift, split_alignment, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, output_mapping_in_SAM, output_mapping_in_pairs, low_memory_mode, cell_by_bin, bin_size, depth_cutoff_to_call_peak, peak_min_length, peak_merge_max_length, reference_file_path, index_file_path, read_file1_paths, read_file2_paths, barcode_file_paths, barcode_whitelist_file_path, output_file_path, matrix_output_prefix, custom_rid_order_path, pairs_custom_rid_order_path);
		chromap_for_mapping.MapPairedEndReads();
		} else if (output_mapping_in_pairs) {
		chromap::Chromap<chromap::PairsMapping> chromap_for_mapping(error_threshold, match_score, mismatch_penalty, gap_open_penalties, gap_extension_penalties, min_num_seeds_required_for_mapping, max_seed_frequencies, max_num_best_mappings, max_insert_size, mapq_threshold, num_threads, min_read_length, multi_mapping_allocation_distance, multi_mapping_allocation_seed, drop_repetitive_reads, trim_adapters, remove_pcr_duplicates, remove_pcr_duplicates_at_bulk_level, is_bulk_data, allocate_multi_mappings, only_output_unique_mappings, Tn5_shift, split_alignment, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, output_mapping_in_SAM, output_mapping_in_pairs, low_memory_mode, cell_by_bin, bin_size, depth_cutoff_to_call_peak, peak_min_length, peak_merge_max_length, reference_file_path, index_file_path, read_file1_paths, read_file2_paths, barcode_file_paths, barcode_whitelist_file_path, output_file_path, matrix_output_prefix, custom_rid_order_path, pairs_custom_rid_order_path);
		chromap::Chromap<chromap::PairsMapping> chromap_for_mapping(error_threshold, match_score, mismatch_penalty, gap_open_penalties, gap_extension_penalties, min_num_seeds_required_for_mapping, max_seed_frequencies, max_num_best_mappings, max_insert_size, mapq_threshold, num_threads, min_read_length, multi_mapping_allocation_distance, multi_mapping_allocation_seed, drop_repetitive_reads, trim_adapters, remove_pcr_duplicates, remove_pcr_duplicates_at_bulk_level, is_bulk_data, allocate_multi_mappings, only_output_unique_mappings, output_mappings_not_in_whitelist, Tn5_shift, split_alignment, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, output_mapping_in_SAM, output_mapping_in_pairs, low_memory_mode, cell_by_bin, bin_size, depth_cutoff_to_call_peak, peak_min_length, peak_merge_max_length, reference_file_path, index_file_path, read_file1_paths, read_file2_paths, barcode_file_paths, barcode_whitelist_file_path, output_file_path, matrix_output_prefix, custom_rid_order_path, pairs_custom_rid_order_path);
		chromap_for_mapping.MapPairedEndReads();
		} else {
		if (result.count("b") != 0) {
		chromap::Chromap<chromap::PairedEndMappingWithBarcode> chromap_for_mapping(error_threshold, match_score, mismatch_penalty, gap_open_penalties, gap_extension_penalties, min_num_seeds_required_for_mapping, max_seed_frequencies, max_num_best_mappings, max_insert_size, mapq_threshold, num_threads, min_read_length, multi_mapping_allocation_distance, multi_mapping_allocation_seed, drop_repetitive_reads, trim_adapters, remove_pcr_duplicates, remove_pcr_duplicates_at_bulk_level, is_bulk_data, allocate_multi_mappings, only_output_unique_mappings, Tn5_shift, split_alignment, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, output_mapping_in_SAM, output_mapping_in_pairs, low_memory_mode, cell_by_bin, bin_size, depth_cutoff_to_call_peak, peak_min_length, peak_merge_max_length, reference_file_path, index_file_path, read_file1_paths, read_file2_paths, barcode_file_paths, barcode_whitelist_file_path, output_file_path, matrix_output_prefix, custom_rid_order_path, pairs_custom_rid_order_path);
		chromap::Chromap<chromap::PairedEndMappingWithBarcode> chromap_for_mapping(error_threshold, match_score, mismatch_penalty, gap_open_penalties, gap_extension_penalties, min_num_seeds_required_for_mapping, max_seed_frequencies, max_num_best_mappings, max_insert_size, mapq_threshold, num_threads, min_read_length, multi_mapping_allocation_distance, multi_mapping_allocation_seed, drop_repetitive_reads, trim_adapters, remove_pcr_duplicates, remove_pcr_duplicates_at_bulk_level, is_bulk_data, allocate_multi_mappings, only_output_unique_mappings, output_mappings_not_in_whitelist, Tn5_shift, split_alignment, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, output_mapping_in_SAM, output_mapping_in_pairs, low_memory_mode, cell_by_bin, bin_size, depth_cutoff_to_call_peak, peak_min_length, peak_merge_max_length, reference_file_path, index_file_path, read_file1_paths, read_file2_paths, barcode_file_paths, barcode_whitelist_file_path, output_file_path, matrix_output_prefix, custom_rid_order_path, pairs_custom_rid_order_path);
		chromap_for_mapping.MapPairedEndReads();
		} else {
		chromap::Chromap<chromap::PairedEndMappingWithoutBarcode> chromap_for_mapping(error_threshold, match_score, mismatch_penalty, gap_open_penalties, gap_extension_penalties, min_num_seeds_required_for_mapping, max_seed_frequencies, max_num_best_mappings, max_insert_size, mapq_threshold, num_threads, min_read_length, multi_mapping_allocation_distance, multi_mapping_allocation_seed, drop_repetitive_reads, trim_adapters, remove_pcr_duplicates, remove_pcr_duplicates_at_bulk_level, is_bulk_data, allocate_multi_mappings, only_output_unique_mappings, Tn5_shift, split_alignment, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, output_mapping_in_SAM, output_mapping_in_pairs, low_memory_mode, cell_by_bin, bin_size, depth_cutoff_to_call_peak, peak_min_length, peak_merge_max_length, reference_file_path, index_file_path, read_file1_paths, read_file2_paths, barcode_file_paths, barcode_whitelist_file_path, output_file_path, matrix_output_prefix, custom_rid_order_path, pairs_custom_rid_order_path);
		chromap::Chromap<chromap::PairedEndMappingWithoutBarcode> chromap_for_mapping(error_threshold, match_score, mismatch_penalty, gap_open_penalties, gap_extension_penalties, min_num_seeds_required_for_mapping, max_seed_frequencies, max_num_best_mappings, max_insert_size, mapq_threshold, num_threads, min_read_length, multi_mapping_allocation_distance, multi_mapping_allocation_seed, drop_repetitive_reads, trim_adapters, remove_pcr_duplicates, remove_pcr_duplicates_at_bulk_level, is_bulk_data, allocate_multi_mappings, only_output_unique_mappings, output_mappings_not_in_whitelist, Tn5_shift, split_alignment, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, output_mapping_in_SAM, output_mapping_in_pairs, low_memory_mode, cell_by_bin, bin_size, depth_cutoff_to_call_peak, peak_min_length, peak_merge_max_length, reference_file_path, index_file_path, read_file1_paths, read_file2_paths, barcode_file_paths, barcode_whitelist_file_path, output_file_path, matrix_output_prefix, custom_rid_order_path, pairs_custom_rid_order_path);
		chromap_for_mapping.MapPairedEndReads();
		}
		}

src/chromap.h

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