Commit 2dd08a6c authored by Haowen Zhang's avatar Haowen Zhang Committed by Li Song
Browse files

Separate headers for mapping and index parameters.

parent 32ae269d

src/chromap.h

+2 −57
Original line number Diff line number Diff line
@@ -12,9 +12,11 @@ 


#include "feature_barcode_matrix_writer.h"

#include "index.h"

#include "index_parameters.h"

#include "khash.h"

#include "ksort.h"

#include "mapping_metadata.h"

#include "mapping_parameters.h"

#include "output_tools.h"

#include "paired_end_mapping_metadata.h"

#include "sequence_batch.h"
@@ -68,63 +70,6 @@ struct BarcodeWithQual { 
  }

};



struct IndexParameters {

  int kmer_size = 17;

  int window_size = 7;

  int num_threads = 1;

  std::string reference_file_path;

  std::string index_output_file_path;

};



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;

  MappingOutputFormat mapping_output_format = MAPPINGFORMAT_BED;

  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;

  std::string barcode_translate_table_path;

  bool skip_barcode_check = false;

};



#define SortMappingWithoutBarcode(m)                                      \

  (((((m).fragment_start_position_ << 16) | (m).fragment_length_) << 8) | \

   (m).mapq_)

src/index_parameters.h

0 → 100644
+16 −0
Original line number Diff line number Diff line 
#ifndef INDEX_PARAMETERS_H_

#define INDEX_PARAMETERS_H_



namespace chromap {



struct IndexParameters {

  int kmer_size = 17;

  int window_size = 7;

  int num_threads = 1;

  std::string reference_file_path;

  std::string index_output_file_path;

};



}  // namespace chromap



#endif  // INDEX_PARAMETERS_H_

src/mapping_parameters.h

0 → 100644
+66 −0
Original line number Diff line number Diff line 
#ifndef MAPPING_PARAMETERS_H_

#define MAPPING_PARAMETERS_H_



namespace chromap {



enum MappingOutputFormat {

  MAPPINGFORMAT_UNKNOWN,

  MAPPINGFORMAT_BED,

  MAPPINGFORMAT_TAGALIGN,

  MAPPINGFORMAT_PAF,

  MAPPINGFORMAT_SAM,

  MAPPINGFORMAT_PAIRS

};



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;

  MappingOutputFormat mapping_output_format = MAPPINGFORMAT_BED;

  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;

  std::string barcode_translate_table_path;

  bool skip_barcode_check = false;

};



}  // namespace chromap



#endif  // MAPPING_PARAMETERS_H_

src/output_tools.h

+1 −9
Original line number Diff line number Diff line
@@ -13,6 +13,7 @@ 
#include "barcode_translator.h"

#include "bed_mapping.h"

#include "mapping.h"

#include "mapping_parameters.h"

#include "paf_mapping.h"

#include "pairs_mapping.h"

#include "sam_mapping.h"
@@ -20,15 +21,6 @@ 


namespace chromap {



enum MappingOutputFormat {

  MAPPINGFORMAT_UNKNOWN,

  MAPPINGFORMAT_BED,

  MAPPINGFORMAT_TAGALIGN,

  MAPPINGFORMAT_PAF,

  MAPPINGFORMAT_SAM,

  MAPPINGFORMAT_PAIRS

};



template <typename MappingRecord>

bool ReadIdLess(const std::pair<uint32_t, MappingRecord> &a,

                const std::pair<uint32_t, MappingRecord> &b) {

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