Commit 636bee27 authored by Li's avatar Li
Browse files

Add the option --read-format for custom read and barcode format.

parent 6e97125b

src/chromap.cc

+27 −11
Original line number Diff line number Diff line
@@ -951,6 +951,12 @@ void Chromap<MappingRecord>::MapPairedEndReads() { 
  SequenceBatch read_batch1_for_loading(read_batch_size_);

  SequenceBatch read_batch2_for_loading(read_batch_size_);

  SequenceBatch barcode_batch_for_loading(read_batch_size_);

	read_batch1.SetSeqEffectiveRange(read1_format_[0], read1_format_[1]);

	read_batch2.SetSeqEffectiveRange(read2_format_[0], read2_format_[1]);

	barcode_batch.SetSeqEffectiveRange(barcode_format_[0], barcode_format_[1]);

	read_batch1_for_loading.SetSeqEffectiveRange(read1_format_[0], read1_format_[1]);

	read_batch2_for_loading.SetSeqEffectiveRange(read2_format_[0], read2_format_[1]);

	barcode_batch_for_loading.SetSeqEffectiveRange(barcode_format_[0], barcode_format_[1]);

  // Initialize cache

  mm_cache mm_to_candidates_cache(2000003);

  mm_to_candidates_cache.SetKmerLength(kmer_size_);
@@ -1913,6 +1919,10 @@ void Chromap<MappingRecord>::MapSingleEndReads() { 
  SequenceBatch read_batch_for_loading(read_batch_size_);

  SequenceBatch barcode_batch(read_batch_size_);

  SequenceBatch barcode_batch_for_loading(read_batch_size_);

	read_batch.SetSeqEffectiveRange(read1_format_[0], read1_format_[1]);

	read_batch_for_loading.SetSeqEffectiveRange(read1_format_[0], read1_format_[1]);

	barcode_batch.SetSeqEffectiveRange(barcode_format_[0], barcode_format_[1]);

	barcode_batch_for_loading.SetSeqEffectiveRange(barcode_format_[0], barcode_format_[1]);

  mappings_on_diff_ref_seqs_.reserve(num_reference_sequences);

  deduped_mappings_on_diff_ref_seqs_.reserve(num_reference_sequences);

  for (uint32_t i = 0; i < num_reference_sequences; ++i) {
@@ -4200,7 +4210,8 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) { 
    ("1,read1", "Single-end read files or paired-end read files 1", cxxopts::value<std::vector<std::string> >(), "FILE")

    ("2,read2", "Paired-end read files 2", cxxopts::value<std::vector<std::string> >(), "FILE")

    ("b,barcode", "Cell barcode files", cxxopts::value<std::vector<std::string> >(), "FILE")

    ("barcode-whitelist", "Cell barcode whitelist file", cxxopts::value<std::string>(), "FILE");

    ("barcode-whitelist", "Cell barcode whitelist file", cxxopts::value<std::string>(), "FILE")

    ("read-format", "Format for read files and barcode files  [\"r1:0:-1,bc:0:-1\" as 10x Genomics single-end format]", cxxopts::value<std::string>(), "STR") ;

  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")
@@ -4523,6 +4534,11 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) { 
        chromap::Chromap<>::ExitWithMessage("No barcode file specified but asked to output matrix files!");

      }

    }

    std::string read_format("");

    if (result.count("read-format")) {

      read_format = result["read-format"].as<std::string>();

    }





    std::string custom_rid_order_path("");

    if (result.count("chr-order")) {
@@ -4621,36 +4637,36 @@ 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, 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::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, read_format, 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, 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::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, read_format, 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, 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::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, read_format, 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, 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::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, read_format, 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, 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::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, read_format, 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, 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::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, read_format, 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, 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::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, read_format, 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, 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::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, read_format, 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, 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::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, read_format, 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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src/sequence_batch.cc

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src/sequence_batch.h

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