Add barcode correction parameters (f28d4df1) · Commits · github_fork / Chromap

src/chromap.cc

+52 −38

Original line number	Diff line number	Diff line
		@@ -131,7 +131,7 @@ bool Chromap<MappingRecord>::CorrectBarcodeAt(uint32_t barcode_index, SequenceBa
		// Correct barcode
		++(*num_barcode_in_whitelist);
		return true;
		} else {
		} else if (barcode_correction_error_threshold_ > 0) {
		// Need to correct this barcode
		//const char *barcode = barcode_batch->GetSequenceAt(barcode_index);
		//std::cerr << barcode_index << " barcode " << barcode << " needs correction\n";
		@@ -161,6 +161,7 @@ bool Chromap<MappingRecord>::CorrectBarcodeAt(uint32_t barcode_index, SequenceBa
		corrected_barcodes_with_quals.emplace_back(BarcodeWithQual{barcode_length - 1 - i, SequenceBatch::Uint8ToChar(base_to_change1), 0, 0, score});
		//std::cerr << "1score: " << score << " pos1: " << barcode_length - 1 - i << " b1: " << base_to_change1 << " pos2: " << 0 << " b2: " << (char)0 << "\n";
		}
		if (barcode_correction_error_threshold_ == 2) {
		for (uint32_t j = i + 1; j < barcode_length; ++j) {
		uint32_t barcode_key_to_change2 = mask << (2 * i);
		barcode_key_to_change2 = mask << (2 * j);
		@@ -193,6 +194,7 @@ bool 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
		@@ -228,7 +230,7 @@ bool Chromap<MappingRecord>::CorrectBarcodeAt(uint32_t barcode_index, SequenceBa
		// best_corrected_barcode_index = distribution(tmp_generator);
		//}
		//std::cerr << "Corrected the barcode from " << barcode << " to ";
		double confidence_threshold = 0.975;
		double confidence_threshold = barcode_correction_probability_threshold_;
		if (corrected_barcodes_with_quals[best_corrected_barcode_index].score / sum_score > confidence_threshold) {
		barcode_batch->CorrectBaseAt(barcode_index, corrected_barcodes_with_quals[best_corrected_barcode_index].corrected_base_index1, corrected_barcodes_with_quals[best_corrected_barcode_index].correct_base1);
		if (corrected_barcodes_with_quals[best_corrected_barcode_index].correct_base2 != 0) {
		@@ -245,6 +247,8 @@ bool Chromap<MappingRecord>::CorrectBarcodeAt(uint32_t barcode_index, SequenceBa
		return false;
		}
		}
		} else {
		return false;
		}
		}

		@@ -4160,6 +4164,8 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		//("allocate-multi-mappings", "Allocate multi-mappings")
		("Tn5-shift", "Perform Tn5 shift")
		("low-mem", "Use low memory mode")
		("bc-error-threshold", "Max Hamming distance allowed to correct a barcode [2]", cxxopts::value<int>(), "INT")
		("bc-probability-threshold", "Min probability to correct a barcode [0.975]", cxxopts::value<double>(), "FLT")
		("t,num-threads", "# threads for mapping [1]", cxxopts::value<int>(), "INT");
		//options.add_options("Peak")
		// ("cell-by-bin", "Generate cell-by-bin matrix")
		@@ -4216,6 +4222,8 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		uint8_t mapq_threshold = 30;
		int num_threads = 1;
		int min_read_length = 30;
		int barcode_correction_error_threshold = 2;
		double barcode_correction_probability_threshold = 0.975;
		int multi_mapping_allocation_distance = 0;
		int multi_mapping_allocation_seed = 11;
		int drop_repetitive_reads = 500000;
		@@ -4317,6 +4325,12 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		if (result.count("min-read-length")) {
		min_read_length = result["min-read-length"].as<int>();
		}
		if (result.count("bc-error-threshold")) {
		barcode_correction_error_threshold = result["bc-error-threshold"].as<int>();
		}
		if (result.count("bc-probability-threshold")) {
		barcode_correction_probability_threshold = result["bc-probability-threshold"].as<double>();
		}
		if (result.count("multi-mapping-allocation-distance")) {
		multi_mapping_allocation_distance = result["multi-mapping-allocation-distance"].as<int>();
		}
		@@ -4570,36 +4584,36 @@ 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, 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::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, barcode_correction_error_threshold, barcode_correction_probability_threshold, 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, 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::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, barcode_correction_error_threshold, barcode_correction_probability_threshold, 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, 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::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, barcode_correction_error_threshold, barcode_correction_probability_threshold, 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, 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::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, barcode_correction_error_threshold, barcode_correction_probability_threshold, 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, 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::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, barcode_correction_error_threshold, barcode_correction_probability_threshold, 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, 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::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, barcode_correction_error_threshold, barcode_correction_probability_threshold, 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, 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::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, barcode_correction_error_threshold, barcode_correction_probability_threshold, 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, 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::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, barcode_correction_error_threshold, barcode_correction_probability_threshold, 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, 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::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, barcode_correction_error_threshold, barcode_correction_probability_threshold, 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

+3 −1

File changed.

Preview size limit exceeded, changes collapsed.

Admin message