Commit 8256b385 authored by Haowen Zhang's avatar Haowen Zhang
Browse files

Use struct to hold mapping parameters.

parent 8efd2283

src/chromap.cc

+217 −402

File changed.

Preview size limit exceeded, changes collapsed.

src/chromap.h

+127 −93
Original line number Diff line number Diff line
@@ -64,6 +64,57 @@ struct BarcodeWithQual { 
  }

};



struct MappingParameters {

  int error_threshold = 8;

  int match_score = 1;

  int mismatch_penalty = 4;

  std::vector<int> gap_open_penalties = {6, 6};

  std::vector<int> gap_extension_penalties = {1, 1};

  int min_num_seeds_required_for_mapping = 2;

  std::vector<int> max_seed_frequencies = {500, 1000};

  int max_num_best_mappings = 1;

  int max_insert_size = 1000;

  uint8_t mapq_threshold = 30;

  int num_threads = 1;

  int min_read_length = 30;

  int barcode_correction_error_threshold = 1;

  double barcode_correction_probability_threshold = 0.9;

  int multi_mapping_allocation_distance = 0;

  int multi_mapping_allocation_seed = 11;

  int drop_repetitive_reads = 500000;

  bool trim_adapters = false;

  bool remove_pcr_duplicates = false;

  bool remove_pcr_duplicates_at_bulk_level = true;

  bool is_bulk_data = true;

  bool allocate_multi_mappings = false;

  bool only_output_unique_mappings = true;

  bool output_mappings_not_in_whitelist = false;

  bool Tn5_shift = false;

  bool split_alignment = false;

  bool output_mapping_in_BED = false;

  bool output_mapping_in_TagAlign = false;

  bool output_mapping_in_PAF = false;

  bool output_mapping_in_SAM = false;

  bool output_mapping_in_pairs = false;

  bool low_memory_mode = false;

  bool cell_by_bin = false;

  int bin_size = 5000;

  uint16_t depth_cutoff_to_call_peak = 3;

  int peak_min_length = 30;

  int peak_merge_max_length = 30;

  std::string reference_file_path;

  std::string index_file_path;

  std::vector<std::string> read_file1_paths;

  std::vector<std::string> read_file2_paths;

  std::vector<std::string> barcode_file_paths;

  std::string barcode_whitelist_file_path;

  std::string read_format;

  std::string mapping_output_file_path;

  std::string matrix_output_prefix;

  std::string custom_rid_order_path;

  std::string pairs_custom_rid_order_path;

};



#define SortMappingWithoutBarcode(m)                                    \

  (((((m).fragment_start_position << 16) | (m).fragment_length) << 8) | \

   (m).mapq)
@@ -95,90 +146,71 @@ class Chromap { 
  }



  // For mapping

  Chromap(int error_threshold, int match_score, int mismatch_penalty,

          const std::vector<int> &gap_open_penalties,

          const std::vector<int> &gap_extension_penalties,

          int min_num_seeds_required_for_mapping,

          const std::vector<int> &max_seed_frequencies,

          int max_num_best_mappings, int max_insert_size,

          uint8_t mapq_threshold, int num_threads, int min_read_length,

          int barcode_correction_error_threshold,

          double barcode_correction_probability_threshold,

          int multi_mapping_allocation_distance,

          int multi_mapping_allocation_seed, int drop_repetitive_reads,

          bool trim_adapters, bool remove_pcr_duplicates,

          bool remove_pcr_duplicates_at_bulk_level, bool is_bulk_data,

          bool allocate_multi_mappings, bool only_output_unique_mappings,

          bool output_mappings_not_in_whitelist, bool Tn5_shift,

          bool split_alignment, bool output_mapping_in_BED,

          bool output_mapping_in_TagAlign, bool output_mapping_in_PAF,

          bool output_mapping_in_SAM, bool output_mapping_in_pairs,

          bool low_memory_mode, bool cell_by_bin, int bin_size,

          uint16_t depth_cutoff_to_call_peak, int peak_min_length,

          int peak_merge_max_length, const std::string &reference_file_path,

          const std::string &index_file_path,

          const std::vector<std::string> &read_file1_paths,

          const std::vector<std::string> &read_file2_paths,

          const std::vector<std::string> &barcode_file_paths,

          const std::string &barcode_whitelist_file_path,

          const std::string &read_format,

          const std::string &mapping_output_file_path,

          const std::string &matrix_output_prefix,

          const std::string &custom_rid_order_path,

          const std::string &pairs_custom_rid_order_path)

      : error_threshold_(error_threshold),

        match_score_(match_score),

        mismatch_penalty_(mismatch_penalty),

        gap_open_penalties_(gap_open_penalties),

        gap_extension_penalties_(gap_extension_penalties),

        min_num_seeds_required_for_mapping_(min_num_seeds_required_for_mapping),

        max_seed_frequencies_(max_seed_frequencies),

        max_num_best_mappings_(max_num_best_mappings),

        max_insert_size_(max_insert_size),

        mapq_threshold_(mapq_threshold),

        num_threads_(num_threads),

        min_read_length_(min_read_length),

        barcode_correction_error_threshold_(barcode_correction_error_threshold),

  Chromap(const MappingParameters &mapping_parameters)

      : error_threshold_(mapping_parameters.error_threshold),

        match_score_(mapping_parameters.match_score),

        mismatch_penalty_(mapping_parameters.mismatch_penalty),

        gap_open_penalties_(mapping_parameters.gap_open_penalties),

        gap_extension_penalties_(mapping_parameters.gap_extension_penalties),

        min_num_seeds_required_for_mapping_(

            mapping_parameters.min_num_seeds_required_for_mapping),

        max_seed_frequencies_(mapping_parameters.max_seed_frequencies),

        max_num_best_mappings_(mapping_parameters.max_num_best_mappings),

        max_insert_size_(mapping_parameters.max_insert_size),

        mapq_threshold_(mapping_parameters.mapq_threshold),

        num_threads_(mapping_parameters.num_threads),

        min_read_length_(mapping_parameters.min_read_length),

        barcode_correction_error_threshold_(

            mapping_parameters.barcode_correction_error_threshold),

        barcode_correction_probability_threshold_(

            barcode_correction_probability_threshold),

        multi_mapping_allocation_distance_(multi_mapping_allocation_distance),

        multi_mapping_allocation_seed_(multi_mapping_allocation_seed),

        drop_repetitive_reads_(drop_repetitive_reads),

        trim_adapters_(trim_adapters),

        remove_pcr_duplicates_(remove_pcr_duplicates),

            mapping_parameters.barcode_correction_probability_threshold),

        multi_mapping_allocation_distance_(

            mapping_parameters.multi_mapping_allocation_distance),

        multi_mapping_allocation_seed_(

            mapping_parameters.multi_mapping_allocation_seed),

        drop_repetitive_reads_(mapping_parameters.drop_repetitive_reads),

        trim_adapters_(mapping_parameters.trim_adapters),

        remove_pcr_duplicates_(mapping_parameters.remove_pcr_duplicates),

        remove_pcr_duplicates_at_bulk_level_(

            remove_pcr_duplicates_at_bulk_level),

        is_bulk_data_(is_bulk_data),

        allocate_multi_mappings_(allocate_multi_mappings),

        only_output_unique_mappings_(only_output_unique_mappings),

        output_mappings_not_in_whitelist_(output_mappings_not_in_whitelist),

        Tn5_shift_(Tn5_shift),

        split_alignment_(split_alignment),

        output_mapping_in_BED_(output_mapping_in_BED),

        output_mapping_in_TagAlign_(output_mapping_in_TagAlign),

        output_mapping_in_PAF_(output_mapping_in_PAF),

        output_mapping_in_SAM_(output_mapping_in_SAM),

        output_mapping_in_pairs_(output_mapping_in_pairs),

        low_memory_mode_(low_memory_mode),

        cell_by_bin_(cell_by_bin),

        bin_size_(bin_size),

        depth_cutoff_to_call_peak_(depth_cutoff_to_call_peak),

        peak_min_length_(peak_min_length),

        peak_merge_max_length_(peak_merge_max_length),

        reference_file_path_(reference_file_path),

        index_file_path_(index_file_path),

        read_file1_paths_(read_file1_paths),

        read_file2_paths_(read_file2_paths),

        barcode_file_paths_(barcode_file_paths),

        barcode_whitelist_file_path_(barcode_whitelist_file_path),

        mapping_output_file_path_(mapping_output_file_path),

        matrix_output_prefix_(matrix_output_prefix),

        custom_rid_order_path_(custom_rid_order_path),

        pairs_custom_rid_order_path_(pairs_custom_rid_order_path) {

            mapping_parameters.remove_pcr_duplicates_at_bulk_level),

        is_bulk_data_(mapping_parameters.is_bulk_data),

        allocate_multi_mappings_(mapping_parameters.allocate_multi_mappings),

        only_output_unique_mappings_(

            mapping_parameters.only_output_unique_mappings),

        output_mappings_not_in_whitelist_(

            mapping_parameters.output_mappings_not_in_whitelist),

        Tn5_shift_(mapping_parameters.Tn5_shift),

        split_alignment_(mapping_parameters.split_alignment),

        output_mapping_in_BED_(mapping_parameters.output_mapping_in_BED),

        output_mapping_in_TagAlign_(

            mapping_parameters.output_mapping_in_TagAlign),

        output_mapping_in_PAF_(mapping_parameters.output_mapping_in_PAF),

        output_mapping_in_SAM_(mapping_parameters.output_mapping_in_SAM),

        output_mapping_in_pairs_(mapping_parameters.output_mapping_in_pairs),

        low_memory_mode_(mapping_parameters.low_memory_mode),

        cell_by_bin_(mapping_parameters.cell_by_bin),

        bin_size_(mapping_parameters.bin_size),

        depth_cutoff_to_call_peak_(

            mapping_parameters.depth_cutoff_to_call_peak),

        peak_min_length_(mapping_parameters.peak_min_length),

        peak_merge_max_length_(mapping_parameters.peak_merge_max_length),

        reference_file_path_(mapping_parameters.reference_file_path),

        index_file_path_(mapping_parameters.index_file_path),

        read_file1_paths_(mapping_parameters.read_file1_paths),

        read_file2_paths_(mapping_parameters.read_file2_paths),

        barcode_file_paths_(mapping_parameters.barcode_file_paths),

        barcode_whitelist_file_path_(

            mapping_parameters.barcode_whitelist_file_path),

        mapping_output_file_path_(mapping_parameters.mapping_output_file_path),

        matrix_output_prefix_(mapping_parameters.matrix_output_prefix),

        custom_rid_order_path_(mapping_parameters.custom_rid_order_path),

        pairs_custom_rid_order_path_(

            mapping_parameters.pairs_custom_rid_order_path) {

    barcode_lookup_table_ = kh_init(k64_seq);

    barcode_whitelist_lookup_table_ = kh_init(k64_seq);

    barcode_histogram_ = kh_init(k64_seq);

    barcode_index_table_ = kh_init(k64_seq);



    NUM_VPU_LANES_ = 0;

    if (error_threshold_ < 8) {

      NUM_VPU_LANES_ = 8;
@@ -186,7 +218,7 @@ class Chromap { 
      NUM_VPU_LANES_ = 4;

    }



    ParseReadFormat(read_format);

    ParseReadFormat(mapping_parameters.read_format);

  }



  ~Chromap() {
@@ -570,8 +602,9 @@ class Chromap { 
  std::vector<int> gap_extension_penalties_;

  int min_num_seeds_required_for_mapping_;

  std::vector<int> max_seed_frequencies_;

  int max_num_best_mappings_;  // Read with # best mappings greater than it will

                               // have this number of best mappings reported.

  // Read with # best mappings greater than it will have this number of best

  // mappings reported.

  int max_num_best_mappings_;

  int max_insert_size_;

  uint8_t mapq_threshold_;

  int num_threads_;
@@ -580,8 +613,8 @@ class Chromap { 
  double barcode_correction_probability_threshold_;

  int multi_mapping_allocation_distance_;

  int multi_mapping_allocation_seed_;

  int drop_repetitive_reads_;  // Read with more than this number of mappings

                               // will be dropped.

  // Read with more than this number of mappings will be dropped.

  int drop_repetitive_reads_;

  bool trim_adapters_;

  bool remove_pcr_duplicates_;

  bool remove_pcr_duplicates_at_bulk_level_;
@@ -596,9 +629,9 @@ class Chromap { 
  bool output_mapping_in_PAF_;

  bool output_mapping_in_SAM_;

  bool output_mapping_in_pairs_;

  uint32_t read_batch_size_ =

      500000;  // default batch size, # reads for single-end reads, # read pairs

               // for paired-end reads

  // Default batch size, # reads for single-end reads, # read pairs for

  // paired-end reads.

  uint32_t read_batch_size_ = 500000;

  bool low_memory_mode_;

  bool cell_by_bin_;

  int bin_size_;
@@ -617,9 +650,10 @@ class Chromap { 
  std::string mapping_output_file_path_;

  FILE *mapping_output_file_;

  std::string matrix_output_prefix_;

  std::string custom_rid_order_path_;  // the order for general sorting

  std::string

      pairs_custom_rid_order_path_;  // the order for pairs format flipping

  // The order for general sorting.

  std::string custom_rid_order_path_;

  // The order for pairs format flipping.

  std::string pairs_custom_rid_order_path_;

  std::vector<int> custom_rid_rank_;

  std::vector<int> pairs_custom_rid_rank_;

  // khash_t(k32_set)* barcode_whitelist_lookup_table_;
@@ -636,10 +670,10 @@ class Chromap { 
  std::vector<std::pair<uint32_t, MappingRecord> > multi_mappings_;

  std::vector<std::vector<MappingRecord> > allocated_mappings_on_diff_ref_seqs_;

  std::vector<std::vector<uint32_t> > tree_extras_on_diff_ref_seqs_;  // max

  std::vector<std::pair<int, uint32_t> >

      tree_info_on_diff_ref_seqs_;  // (max_level, # nodes)

  // (max_level, # nodes)

  std::vector<std::pair<int, uint32_t> > tree_info_on_diff_ref_seqs_;

  std::unique_ptr<OutputTools<MappingRecord> > output_tools_;

  // For mapping stats

  // For mapping stats.

  uint64_t num_candidates_ = 0;

  uint64_t num_mappings_ = 0;

  uint64_t num_mapped_reads_ = 0;

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