Commit e4645bae authored by Li's avatar Li
Browse files

Add the format pairs for hic data analysis

parent 63e039ce

src/chromap.cc

+50 −8
Original line number Diff line number Diff line
@@ -770,6 +770,8 @@ void Chromap<MappingRecord>::MapPairedEndReads() { 
    output_tools_ = std::unique_ptr<PairedPAFOutputTools<MappingRecord> >(new PairedPAFOutputTools<MappingRecord>);

  } else if (output_mapping_in_SAM_) {

    output_tools_ = std::unique_ptr<SAMOutputTools<MappingRecord> >(new SAMOutputTools<MappingRecord>);

  } else if (output_mapping_in_pairs_) {

    output_tools_ = std::unique_ptr<PairsOutputTools<MappingRecord> >(new PairsOutputTools<MappingRecord>);

  }

  output_tools_->InitializeMappingOutput(mapping_output_file_path_);

  output_tools_->OutputHeader(num_reference_sequences, reference);
@@ -1402,6 +1404,15 @@ void Chromap<PairedPAFMapping>::EmplaceBackMappingRecord(uint32_t read_id, const 
  mappings_on_diff_ref_seqs->emplace_back(PairedPAFMapping{read_id, std::string(read1_name), std::string(read2_name), read1_length, read2_length, fragment_start_position, fragment_length, positive_alignment_length, negative_alignment_length, mapq1 < mapq2 ? mapq1 : mapq2, mapq1, mapq2, direction, is_unique, num_dups});

}



template<typename MappingRecord>

void Chromap<MappingRecord>::EmplaceBackMappingRecord(uint32_t read_id, const char *read_name, uint32_t cell_barcode, int rid1, int rid2, uint32_t pos1, uint32_t pos2, int direction1, int direction2, uint8_t mapq, uint8_t is_unique, uint8_t num_dups, std::vector<MappingRecord> *mappings_on_diff_ref_seqs) {

}



template<>

void Chromap<PairsMapping>::EmplaceBackMappingRecord(uint32_t read_id, const char *read_name, uint32_t cell_barcode, int rid1, int rid2, uint32_t pos1, uint32_t pos2, int direction1, int direction2, uint8_t mapq, uint8_t is_unique, uint8_t num_dups, std::vector<PairsMapping> *mappings_on_diff_ref_seqs) {

  mappings_on_diff_ref_seqs->emplace_back(PairsMapping{read_id, std::string(read_name), cell_barcode, rid1, rid2, pos1, pos2, direction1, direction2, mapq, is_unique, num_dups});

}



template <typename MappingRecord>

void Chromap<MappingRecord>::ProcessBestMappingsForPairedEndReadOnOneDirection(Direction first_read_direction, uint32_t pair_index, uint8_t mapq, int num_candidates1, uint32_t repetitive_seed_length1, int min_num_errors1, int num_best_mappings1, int second_min_num_errors1, int num_second_best_mappings1, const SequenceBatch &read_batch1, const std::vector<std::pair<int, uint64_t> > &mappings1, const std::vector<int> &split_sites1, int num_candidates2, uint32_t repetitive_seed_length2, int min_num_errors2, int num_best_mappings2, int second_min_num_errors2, int num_second_best_mappings2, const SequenceBatch &read_batch2, const SequenceBatch &reference, const SequenceBatch &barcode_batch, const std::vector<int> &best_mapping_indices, const std::vector<std::pair<int, uint64_t> > &mappings2, const std::vector<int> &split_sites2, const std::vector<std::pair<uint32_t, uint32_t> > &best_mappings, int min_sum_errors, int num_best_mappings, int second_min_sum_errors, int num_second_best_mappings, int *best_mapping_index, int *num_best_mappings_reported, std::vector<std::vector<MappingRecord> > *mappings_on_diff_ref_seqs) {

	const char *read1 = read_batch1.GetSequenceAt(pair_index);
@@ -1490,6 +1501,27 @@ void Chromap<MappingRecord>::ProcessBestMappingsForPairedEndReadOnOneDirection(D 
				//printf("%d %d\n", ref_start_position2, ref_end_position2);

				  EmplaceBackMappingRecord(read_id, read1_name, 1, ref_start_position1, rid1, flag1, 0, is_unique, mapq, NM1, n_cigar1, cigar1, MD_tag1, &((*mappings_on_diff_ref_seqs)[rid1])); 

				  EmplaceBackMappingRecord(read_id, read2_name, 1, ref_start_position2, rid2, flag2, 0, is_unique, mapq, NM2, n_cigar2, cigar2, MD_tag2, &((*mappings_on_diff_ref_seqs)[rid2])); 

				} else if (output_mapping_in_pairs_) {

					int pos_rid = rid1;

					int neg_rid = rid2;

					int pos_position = ref_start_position1;

					int neg_position = ref_end_position2;

					if (direction == 0) {

						pos_rid = rid2;

						neg_rid = rid1;

						pos_position = ref_start_position2;

						neg_position = ref_end_position1;

					}



					if (pos_rid < neg_rid || (pos_rid == neg_rid && pos_position < neg_position)) {

						EmplaceBackMappingRecord(read_id, read1_name, barcode_key, 

							pos_rid, neg_rid, pos_position, neg_position, 1, 0, mapq, is_unique, 1,

							&((*mappings_on_diff_ref_seqs)[pos_rid])) ;

					} else {

						EmplaceBackMappingRecord(read_id, read1_name, barcode_key, 

							neg_rid, pos_rid, neg_position, pos_position, 0, 1, mapq, is_unique, 1,

							&((*mappings_on_diff_ref_seqs)[neg_rid])) ;

					}

				} else if (output_mapping_in_PAF_) {

					uint32_t fragment_start_position = ref_start_position1;

					uint16_t fragment_length = ref_end_position2 - ref_start_position1 + 1;;
@@ -3535,6 +3567,7 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) { 
    ("drop-repetitive-reads", "Drop reads with too many best mappings [500000]", cxxopts::value<int>(), "INT")

    ("allocate-multi-mappings", "Allocate multi-mappings")

    ("split-alignment", "Allow split alignments")

    ("pairs", "Output mappings in pairs format (defined by 4DN for HiC data)")

    ("SAM", "Output mappings in SAM format (only for test)")

    ("PAF", "Output mappings in PAF format (only for test)");
@@ -3646,6 +3679,10 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) { 
  if (result.count("SAM")) {

    output_mapping_in_SAM = true;

  }

  bool output_mapping_in_pairs = false;

  if (result.count("pairs")) {

    output_mapping_in_pairs = true;

  }

  bool low_memory_mode = false;

  if (result.count("low-mem")) {

    low_memory_mode = true;
@@ -3788,6 +3825,8 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) { 
      std::cerr << "Output mappings in PAF format.\n";

    } else if (output_mapping_in_SAM) {

      std::cerr << "Output mappings in SAM format.\n";

    } else if (output_mapping_in_pairs) {

      std::cerr << "Output mappings in pairs format.\n"; 

    } else {

      chromap::Chromap<>::ExitWithMessage("No output format specified!");

    }
@@ -3815,33 +3854,36 @@ 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, 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, 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);

        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, 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);

        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, 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, 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);

        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, 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);

        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, 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, 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);

          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, 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);

          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, 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, 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);

          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, 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);

          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, 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, 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);

        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, 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);

        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, 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, 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);

        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, 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);

        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, 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);

        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, 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, 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);

          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, 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);

          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, 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, 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);

          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, 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);

          chromap_for_mapping.MapPairedEndReads();

        }

      }

src/chromap.h

+3 −1

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src/output_tools.h

+77 −1

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