Commit 6a39b40a authored by Haowen Zhang's avatar Haowen Zhang
Browse files

Easier way to pass parameters to avoid bugs.

parent 43ddcdfa

src/chromap.cc

+165 −162

File changed.

Preview size limit exceeded, changes collapsed.

src/chromap.h

+7 −125
Original line number Original line Diff line number Diff line
@@ -36,84 +36,17 @@ class Chromap { 
 public:

 public:

  // For index construction

  // For index construction

  Chromap(const IndexParameters &index_parameters)

  Chromap(const IndexParameters &index_parameters)

      : kmer_size_(index_parameters.kmer_size),

      : index_parameters_(index_parameters) {

        window_size_(index_parameters.window_size),

        num_threads_(index_parameters.num_threads),

        reference_file_path_(index_parameters.reference_file_path),

        index_file_path_(index_parameters.index_output_file_path) {

    barcode_lookup_table_ = NULL;

    barcode_lookup_table_ = NULL;

    barcode_whitelist_lookup_table_ = NULL;

    barcode_whitelist_lookup_table_ = NULL;

  }

  }





  // For mapping

  // For mapping

  Chromap(const MappingParameters &mapping_parameters)

  Chromap(const MappingParameters &mapping_parameters)

      : error_threshold_(mapping_parameters.error_threshold),

      : mapping_parameters_(mapping_parameters) {

        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_(

            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_(

            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),

        mapping_output_format_(mapping_parameters.mapping_output_format),

        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_translate_table_path_(

            mapping_parameters.barcode_translate_table_path),

        skip_barcode_check_(mapping_parameters.skip_barcode_check) {

    barcode_lookup_table_ = kh_init(k64_seq);

    barcode_lookup_table_ = kh_init(k64_seq);

    barcode_whitelist_lookup_table_ = kh_init(k64_seq);

    barcode_whitelist_lookup_table_ = kh_init(k64_seq);





    NUM_VPU_LANES_ = 0;

    if (error_threshold_ < 8) {

      NUM_VPU_LANES_ = 8;

    } else if (error_threshold_ < 16) {

      NUM_VPU_LANES_ = 4;

    }



    ParseReadFormat(mapping_parameters.read_format);

    ParseReadFormat(mapping_parameters.read_format);

  }

  }
@@ -185,74 +118,23 @@ class Chromap { 
  void ParseReadFormat(const std::string &read_format);

  void ParseReadFormat(const std::string &read_format);





  // Parameters

  // Parameters

  int kmer_size_;

  const IndexParameters index_parameters_;

  int window_size_;

  const MappingParameters mapping_parameters_;

  int error_threshold_;

  int NUM_VPU_LANES_;

  int match_score_;

  int mismatch_penalty_;

  std::vector<int> gap_open_penalties_;

  std::vector<int> gap_extension_penalties_;

  int min_num_seeds_required_for_mapping_;

  std::vector<int> max_seed_frequencies_;

  // 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_;

  int min_read_length_;

  int barcode_correction_error_threshold_;

  double barcode_correction_probability_threshold_;

  int multi_mapping_allocation_distance_;

  int multi_mapping_allocation_seed_;

  // 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_;

  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_;

  MappingOutputFormat mapping_output_format_;

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

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

  // paired-end reads.

  // paired-end reads.

  uint32_t read_batch_size_ = 500000;

  const uint32_t read_batch_size_ = 500000;

  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_;

  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_;

  // 0-start, 1-end (includsive), 2-strand(-1:minus, 1:plus)

  // 0-start, 1-end (includsive), 2-strand(-1:minus, 1:plus)

  int barcode_format_[3];

  int barcode_format_[3];

  int read1_format_[3];

  int read1_format_[3];

  int read2_format_[3];

  int read2_format_[3];

  std::string mapping_output_file_path_;

  std::string matrix_output_prefix_;

  // 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> custom_rid_rank_;

  std::vector<int> pairs_custom_rid_rank_;

  std::vector<int> pairs_custom_rid_rank_;

  std::string barcode_translate_table_path_;

  khash_t(k64_seq) * barcode_whitelist_lookup_table_;

  khash_t(k64_seq) * barcode_whitelist_lookup_table_;

  // For identical read dedupe

  // For identical read dedupe

  int allocated_barcode_lookup_table_size_ = (1 << 10);

  khash_t(k64_seq) * barcode_lookup_table_;

  khash_t(k64_seq) * barcode_lookup_table_;

  std::vector<khash_t(k128) *> read_lookup_tables_;

  std::vector<khash_t(k128) *> read_lookup_tables_;

  // For mapping

  // For mapping

  int min_unique_mapping_mapq_ = 4;

  const int min_unique_mapping_mapq_ = 4;

  // For mapping stats.

  // For mapping stats.

  uint64_t num_candidates_ = 0;

  uint64_t num_candidates_ = 0;

  uint64_t num_mappings_ = 0;

  uint64_t num_mappings_ = 0;
@@ -261,7 +143,7 @@ class Chromap { 
  uint64_t num_reads_ = 0;

  uint64_t num_reads_ = 0;

  uint64_t num_duplicated_reads_ = 0;  // # identical reads

  uint64_t num_duplicated_reads_ = 0;  // # identical reads

  // For barcode stats

  // For barcode stats

  uint64_t initial_num_sample_barcodes_ = 20000000;

  const uint64_t initial_num_sample_barcodes_ = 20000000;

  uint64_t num_sample_barcodes_ = 0;

  uint64_t num_sample_barcodes_ = 0;

  uint64_t num_barcode_in_whitelist_ = 0;

  uint64_t num_barcode_in_whitelist_ = 0;

  uint64_t num_corrected_barcode_ = 0;

  uint64_t num_corrected_barcode_ = 0;

src/mapping_generator.h

+339 −274

File changed.

Preview size limit exceeded, changes collapsed.

src/mapping_parameters.h

+16 −1
Original line number Original line Diff line number Diff line
@@ -20,6 +20,8 @@ struct MappingParameters { 
  std::vector<int> gap_extension_penalties = {1, 1};

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

  int min_num_seeds_required_for_mapping = 2;

  int min_num_seeds_required_for_mapping = 2;

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

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

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

  // mappings reported.

  int max_num_best_mappings = 1;

  int max_num_best_mappings = 1;

  int max_insert_size = 1000;

  int max_insert_size = 1000;

  uint8_t mapq_threshold = 30;

  uint8_t mapq_threshold = 30;
@@ -29,6 +31,7 @@ struct MappingParameters { 
  double barcode_correction_probability_threshold = 0.9;

  double barcode_correction_probability_threshold = 0.9;

  int multi_mapping_allocation_distance = 0;

  int multi_mapping_allocation_distance = 0;

  int multi_mapping_allocation_seed = 11;

  int multi_mapping_allocation_seed = 11;

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

  int drop_repetitive_reads = 500000;

  int drop_repetitive_reads = 500000;

  bool trim_adapters = false;

  bool trim_adapters = false;

  bool remove_pcr_duplicates = false;

  bool remove_pcr_duplicates = false;
@@ -55,10 +58,22 @@ struct MappingParameters { 
  std::string read_format;

  std::string read_format;

  std::string mapping_output_file_path;

  std::string mapping_output_file_path;

  std::string matrix_output_prefix;

  std::string matrix_output_prefix;

  // The order for general sorting.

  std::string custom_rid_order_path;

  std::string custom_rid_order_path;

  // The order for pairs format flipping.

  std::string pairs_custom_rid_order_path;

  std::string pairs_custom_rid_order_path;

  std::string barcode_translate_table_path;

  std::string barcode_translate_table_file_path;

  bool skip_barcode_check = false;

  bool skip_barcode_check = false;



  int GetNumVPULanes() const {

    int NUM_VPU_LANES = 0;

    if (error_threshold < 8) {

      NUM_VPU_LANES = 8;

    } else if (error_threshold < 16) {

      NUM_VPU_LANES = 4;

    }

    return NUM_VPU_LANES;

  }

};

};





}  // namespace chromap

}  // namespace chromap

src/mapping_processor.h

+8 −7
Original line number Original line Diff line number Diff line
@@ -12,6 +12,7 @@ 




#include "bed_mapping.h"

#include "bed_mapping.h"

#include "mapping.h"

#include "mapping.h"

#include "mapping_parameters.h"

#include "paf_mapping.h"

#include "paf_mapping.h"

#include "pairs_mapping.h"

#include "pairs_mapping.h"

#include "sam_mapping.h"

#include "sam_mapping.h"
@@ -32,14 +33,14 @@ template <typename MappingRecord> 
class MappingProcessor {

class MappingProcessor {

 public:

 public:

  MappingProcessor() = delete;

  MappingProcessor() = delete;

  MappingProcessor(int min_unique_mapping_mapq,

  MappingProcessor(const MappingParameters &mapping_parameters,

                   int multi_mapping_allocation_seed,

                   int min_unique_mapping_mapq)

                   int multi_mapping_allocation_distance,

                   int max_num_best_mappings)

      : min_unique_mapping_mapq_(min_unique_mapping_mapq),

      : min_unique_mapping_mapq_(min_unique_mapping_mapq),

        multi_mapping_allocation_seed_(multi_mapping_allocation_seed),

        multi_mapping_allocation_seed_(

        multi_mapping_allocation_distance_(multi_mapping_allocation_distance),

            mapping_parameters.multi_mapping_allocation_seed),

        max_num_best_mappings_(max_num_best_mappings) {}

        multi_mapping_allocation_distance_(

            mapping_parameters.multi_mapping_allocation_distance),

        max_num_best_mappings_(mapping_parameters.max_num_best_mappings) {}





  ~MappingProcessor() = default;

  ~MappingProcessor() = default;

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