Commit 3aa9cc1c authored by Haowen Zhang's avatar Haowen Zhang
Browse files

Low mem mode

parent 4531386f

src/chromap.cc

+160 −37
Original line number Diff line number Diff line
@@ -521,6 +521,8 @@ void Chromap<MappingRecord>::MapPairedEndReads() { 
    output_tools_ = std::unique_ptr<PairedPAFOutputTools<MappingRecord> >(new PairedPAFOutputTools<MappingRecord>);

  }

  output_tools_->InitializeMappingOutput(mapping_output_file_path_);

  uint32_t num_mappings_in_mem = 0;

  uint64_t max_num_mappings_in_mem = 1 * ((uint64_t)1 << 30) / sizeof(MappingRecord);

  static uint64_t thread_num_candidates = 0;

  static uint64_t thread_num_mappings = 0;

  static uint64_t thread_num_mapped_reads = 0;
@@ -528,7 +530,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() { 
  static uint64_t thread_num_barcode_in_whitelist = 0; 

  static uint64_t thread_num_corrected_barcode = 0; 

#pragma omp threadprivate(thread_num_candidates, thread_num_mappings, thread_num_mapped_reads, thread_num_uniquely_mapped_reads, thread_num_barcode_in_whitelist, thread_num_corrected_barcode)

#pragma omp parallel default(none) shared(reference, index, read_batch1, read_batch2, barcode_batch, read_batch1_for_loading, read_batch2_for_loading, barcode_batch_for_loading, std::cerr, num_loaded_pairs_for_loading, num_loaded_pairs, num_reference_sequences, mappings_on_diff_ref_seqs_for_diff_threads, mappings_on_diff_ref_seqs_for_diff_threads_for_saving) num_threads(num_threads_) reduction(+:num_candidates_, num_mappings_, num_mapped_reads_, num_uniquely_mapped_reads_, num_barcode_in_whitelist_, num_corrected_barcode_)

#pragma omp parallel default(none) shared(reference, index, read_batch1, read_batch2, barcode_batch, read_batch1_for_loading, read_batch2_for_loading, barcode_batch_for_loading, std::cerr, num_loaded_pairs_for_loading, num_loaded_pairs, num_reference_sequences, mappings_on_diff_ref_seqs_for_diff_threads, mappings_on_diff_ref_seqs_for_diff_threads_for_saving, num_mappings_in_mem, max_num_mappings_in_mem, temp_mapping_file_handles_) num_threads(num_threads_) reduction(+:num_candidates_, num_mappings_, num_mapped_reads_, num_uniquely_mapped_reads_, num_barcode_in_whitelist_, num_corrected_barcode_)

  {

  std::vector<std::pair<uint64_t, uint64_t> > minimizers1;

  std::vector<std::pair<uint64_t, uint64_t> > minimizers2;
@@ -655,7 +657,18 @@ void Chromap<MappingRecord>::MapPairedEndReads() { 
    mappings_on_diff_ref_seqs_for_diff_threads.swap(mappings_on_diff_ref_seqs_for_diff_threads_for_saving);

#pragma omp task

    {

    MoveMappingsInBuffersToMappingContainer(num_reference_sequences, &mappings_on_diff_ref_seqs_for_diff_threads_for_saving);

    num_mappings_in_mem += MoveMappingsInBuffersToMappingContainer(num_reference_sequences, &mappings_on_diff_ref_seqs_for_diff_threads_for_saving);

    if (low_memory_mode_ && num_mappings_in_mem > max_num_mappings_in_mem) {

      TempMappingFileHandle<MappingRecord> temp_mapping_file_handle;

      temp_mapping_file_handle.file_path = mapping_output_file_path_ + ".temp" + std::to_string(temp_mapping_file_handles_.size());

      temp_mapping_file_handles_.emplace_back(temp_mapping_file_handle);

      SortOutputMappings(num_reference_sequences, &mappings_on_diff_ref_seqs_);

      output_tools_-> OutputTempMapping(temp_mapping_file_handle.file_path, num_reference_sequences, mappings_on_diff_ref_seqs_);

      num_mappings_in_mem = 0;

      for (uint32_t i = 0; i < num_reference_sequences; ++i) {

        mappings_on_diff_ref_seqs_[i].clear();

      }

    }

    }

    std::cerr << "Mapped in " << Chromap<>::GetRealTime() - real_batch_start_time << "s.\n";

  }
@@ -674,6 +687,106 @@ void Chromap<MappingRecord>::MapPairedEndReads() { 
  }

  std::cerr << "Mapped all reads in " << Chromap<>::GetRealTime() - real_start_mapping_time << "s.\n";

  OutputMappingStatistics();

  if (low_memory_mode_) {

    index.Destroy();

    //for (uint32_t i = 0; i < 4; ++i) {

    //  TempMappingFileHandle<MappingRecord> temp_mapping_file_handle;

    //  temp_mapping_file_handle.file_path = "/nv/hswarm1/hzhang639/scratch/pbmc10k_low_mem.bed.temp" + std::to_string(temp_mapping_file_handles_.size());

    //  temp_mapping_file_handles_.emplace_back(temp_mapping_file_handle);

    //}

    if (num_mappings_in_mem > 0) {

      TempMappingFileHandle<MappingRecord> temp_mapping_file_handle;

      temp_mapping_file_handle.file_path = mapping_output_file_path_ + ".temp" + std::to_string(temp_mapping_file_handles_.size());

      temp_mapping_file_handles_.emplace_back(temp_mapping_file_handle);

      SortOutputMappings(num_reference_sequences, &mappings_on_diff_ref_seqs_);

      double output_temp_mapping_start_time = Chromap<>::GetRealTime();

      output_tools_-> OutputTempMapping(temp_mapping_file_handle.file_path, num_reference_sequences, mappings_on_diff_ref_seqs_);

      std::cerr << "Output temp mappings in " << Chromap<>::GetRealTime() - output_temp_mapping_start_time << "s.\n";

      num_mappings_in_mem = 0;

      for (uint32_t i = 0; i < num_reference_sequences; ++i) {

        mappings_on_diff_ref_seqs_[i].clear();

      }

    }

    double sort_and_dedupe_start_time = Chromap<>::GetRealTime();

    // Calculate block size and initialize

    uint64_t max_mem_size = 10 * ((uint64_t)1 << 30);

    for (size_t hi = 0; hi < temp_mapping_file_handles_.size(); ++hi) {

      temp_mapping_file_handles_[hi].block_size = max_mem_size / temp_mapping_file_handles_.size() / sizeof(MappingRecord);

      temp_mapping_file_handles_[hi].InitializeTempMappingLoading(num_reference_sequences);

      temp_mapping_file_handles_[hi].LoadTempMappingBlock(num_reference_sequences);

    }

    // Merge and dedupe

    bool all_merged = false;

    uint32_t last_rid = std::numeric_limits<uint32_t>::max();

    MappingRecord last_mapping;

    uint8_t dup_count = 0;

    while (!all_merged) {

      // Merge, dedupe and output

      // Find min first (sorted by rid and then barcode and then positions)

      size_t min_handle_index = temp_mapping_file_handles_.size();

      uint32_t min_rid = std::numeric_limits<uint32_t>::max();

      for (size_t hi = 0; hi < temp_mapping_file_handles_.size(); ++hi) {

        TempMappingFileHandle<MappingRecord> &current_handle = temp_mapping_file_handles_[hi];

        if (!current_handle.all_loaded) {

          if (min_handle_index == temp_mapping_file_handles_.size() || current_handle.current_rid < min_rid || (current_handle.current_rid == min_rid && current_handle.mappings[current_handle.current_mapping_index] < temp_mapping_file_handles_[min_handle_index].mappings[temp_mapping_file_handles_[min_handle_index].current_mapping_index])) {

            min_handle_index = hi;

            min_rid = current_handle.current_rid;

          }

        }

      }

      // Append current min to mappings if not a duplicate

      if (min_handle_index != temp_mapping_file_handles_.size()) {

        MappingRecord &current_min_mapping = temp_mapping_file_handles_[min_handle_index].mappings[temp_mapping_file_handles_[min_handle_index].current_mapping_index];

        if (last_rid == min_rid && current_min_mapping == last_mapping) {

          ++dup_count;

        } else {

          if (dup_count > 0) {

            if (last_mapping.mapq >= mapq_threshold_) {

              if (allocate_multi_mappings_ || (only_output_unique_mappings_ && last_mapping.is_unique == 1)) {

                last_mapping.num_dups = dup_count;

                if (Tn5_shift_) {

                  last_mapping.fragment_start_position += 4;

                  last_mapping.positive_alignment_length -= 4;

                  last_mapping.fragment_length -= 9;

                  last_mapping.negative_alignment_length -= 5;

                }

                output_tools_->AppendMapping(last_rid, reference, last_mapping);

              }

            }

          }

          last_mapping = current_min_mapping;

          last_rid = min_rid;

          dup_count = 1;

        }

        temp_mapping_file_handles_[min_handle_index].Next(num_reference_sequences);

      }

      // Check if all are merged.

      all_merged = true;

      for (size_t hi = 0; hi < temp_mapping_file_handles_.size(); ++hi) {

        if (!temp_mapping_file_handles_[hi].all_loaded) {

          all_merged = false;

        }

      }

    }

    if (last_mapping.mapq >= mapq_threshold_) {

      if (allocate_multi_mappings_ || (only_output_unique_mappings_ && last_mapping.is_unique == 1)) {

        last_mapping.num_dups = dup_count;

        if (Tn5_shift_) {

          last_mapping.fragment_start_position += 4;

          last_mapping.positive_alignment_length -= 4;

          last_mapping.fragment_length -= 9;

          last_mapping.negative_alignment_length -= 5;

        }

        output_tools_->AppendMapping(last_rid, reference, last_mapping);

      }

    }

    for (size_t hi = 0; hi < temp_mapping_file_handles_.size(); ++hi) {

      temp_mapping_file_handles_[hi].FinalizeTempMappingLoading();

      remove(temp_mapping_file_handles_[hi].file_path.c_str());

    }

    std::cerr << "Sorted, deduped and outputed mappings in " << Chromap<>::GetRealTime() - sort_and_dedupe_start_time << "s.\n";

    // Delete temp files

  } else {

    OutputMappingStatistics(num_reference_sequences, mappings_on_diff_ref_seqs_, mappings_on_diff_ref_seqs_);

    if (!is_bulk_data_) {

      OutputBarcodeStatistics();
@@ -703,6 +816,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() { 
      OutputFeatureMatrix(num_reference_sequences, reference);

      output_tools_->FinalizeMatrixOutput();

    }

  }

  output_tools_->FinalizeMappingOutput();

  reference.FinalizeLoading();

  std::cerr << "Total time: " << Chromap<>::GetRealTime() - real_start_time << "s.\n";
@@ -1368,15 +1482,18 @@ void Chromap<MappingRecord>::ConstructIndex() { 
}



template <typename MappingRecord>

void Chromap<MappingRecord>::MoveMappingsInBuffersToMappingContainer(uint32_t num_reference_sequences, std::vector<std::vector<std::vector<MappingRecord> > > *mappings_on_diff_ref_seqs_for_diff_threads_for_saving) {

uint32_t Chromap<MappingRecord>::MoveMappingsInBuffersToMappingContainer(uint32_t num_reference_sequences, std::vector<std::vector<std::vector<MappingRecord> > > *mappings_on_diff_ref_seqs_for_diff_threads_for_saving) {

  double real_start_time = Chromap<>::GetRealTime();

  uint32_t num_moved_mappings = 0;

  for (int ti = 0; ti < num_threads_; ++ti) {

    for (uint32_t i = 0; i < num_reference_sequences; ++i) {

      num_moved_mappings += (*mappings_on_diff_ref_seqs_for_diff_threads_for_saving)[ti][i].size();

      mappings_on_diff_ref_seqs_[i].insert(mappings_on_diff_ref_seqs_[i].end(), std::make_move_iterator((*mappings_on_diff_ref_seqs_for_diff_threads_for_saving)[ti][i].begin()), std::make_move_iterator((*mappings_on_diff_ref_seqs_for_diff_threads_for_saving)[ti][i].end()));

      (*mappings_on_diff_ref_seqs_for_diff_threads_for_saving)[ti][i].clear();

    }

  }

  std::cerr << "Move mappings in " << Chromap<>::GetRealTime() - real_start_time << "s.\n";

  return num_moved_mappings;

}



template <typename MappingRecord>
@@ -1405,7 +1522,7 @@ void Chromap<MappingRecord>::RemovePCRDuplicate(uint32_t num_reference_sequences 
  num_mappings = 0;

  for (uint32_t ri = 0; ri < num_reference_sequences; ++ri) {

    if (mappings_on_diff_ref_seqs_[ri].size() != 0) {

      deduped_mappings_on_diff_ref_seqs_[ri].emplace_back(mappings_on_diff_ref_seqs_[ri].front());

      deduped_mappings_on_diff_ref_seqs_[ri].emplace_back(mappings_on_diff_ref_seqs_[ri].front()); // ideally I should output the last of the dups of first mappings.

      //std::vector<MappingRecord>::iterator last_it = mappings_on_diff_ref_seqs_[ri].begin();

      auto last_it = mappings_on_diff_ref_seqs_[ri].begin();

      uint8_t last_dup_count = 1;
@@ -1421,6 +1538,7 @@ void Chromap<MappingRecord>::RemovePCRDuplicate(uint32_t num_reference_sequences 
          ++last_dup_count;

        }

      }

      deduped_mappings_on_diff_ref_seqs_[ri].back().num_dups = last_dup_count;

      std::vector<MappingRecord>().swap(mappings_on_diff_ref_seqs_[ri]);

      num_mappings += deduped_mappings_on_diff_ref_seqs_[ri].size();

    }
@@ -2287,6 +2405,7 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) { 
    ("remove-pcr-duplicates", "Remove PCR duplicates")

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

    ("Tn5-shift", "Perform Tn5 shift")

    ("low-mem", "Use low memory mode")

    ("t,num-threads", "# threads for mapping [1]", cxxopts::value<int>(), "INT");

  options.add_options("Peak")

    ("cell-by-bin", "Generate cell-by-bin matrix")
@@ -2421,6 +2540,10 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) { 
  if (result.count("PAF")) {

    output_mapping_in_PAF = true;

  }

  bool low_memory_mode = false;

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

    low_memory_mode = true;

  }

  bool cell_by_bin = false;

  if (result.count("cell-by-bin")) {

    cell_by_bin = true;
@@ -2574,27 +2697,27 @@ 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, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, 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_path, read_file2_path, barcode_file_path, 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, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, 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_path, read_file2_path, barcode_file_path, 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, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, 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_path, read_file2_path, barcode_file_path, 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, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, 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_path, read_file2_path, barcode_file_path, 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, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, 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_path, read_file2_path, barcode_file_path, 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, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, 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_path, read_file2_path, barcode_file_path, 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, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, 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_path, read_file2_path, barcode_file_path, 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, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, 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_path, read_file2_path, barcode_file_path, 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, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, 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_path, read_file2_path, barcode_file_path, 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, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, 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_path, read_file2_path, barcode_file_path, 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, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, 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_path, read_file2_path, barcode_file_path, 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, output_mapping_in_BED, output_mapping_in_TagAlign, output_mapping_in_PAF, 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_path, read_file2_path, barcode_file_path, barcode_whitelist_file_path, output_file_path, matrix_output_prefix);

          chromap_for_mapping.MapPairedEndReads();

        }

      }

src/chromap.h

+4 −2

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src/index.h

+7 −0
Original line number Diff line number Diff line
@@ -21,8 +21,15 @@ class Index { 
    lookup_table_ = kh_init(k64);

  }

  ~Index(){

    if (lookup_table_ != NULL) {

      kh_destroy(k64, lookup_table_);

    }

  }

  void Destroy() {

    kh_destroy(k64, lookup_table_);

    lookup_table_ = NULL;

    std::vector<uint64_t>().swap(occurrence_table_); 

  }

  khash_t(k64) const * GetLookupTable() const {

    return lookup_table_;

  }

src/output_tools.h

+94 −0

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