Commit 570947e7 authored by Haowen Zhang's avatar Haowen Zhang Committed by Li Song
Browse files

Add generator back as a parameter. 

We have to investigate the difference in the mappings once we remove it
as a parameter.
parent f3dafda0

src/chromap.cc

+2 −1
Original line number Diff line number Diff line
@@ -961,6 +961,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() { 
      PairedEndMappingMetadata paired_end_mapping_metadata;



      std::vector<int> best_mapping_indices(max_num_best_mappings_);

      std::mt19937 generator(11);

#pragma omp single

      {

        double real_batch_start_time = GetRealTime();
@@ -1155,7 +1156,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() { 


                    mapping_generator.GenerateBestMappingsForPairedEndRead(

                        pair_index, read_batch1, read_batch2, barcode_batch,

                        reference, best_mapping_indices, force_mapq,

                        reference, best_mapping_indices, generator, force_mapq,

                        paired_end_mapping_metadata, mappings_on_diff_ref_seqs);



                    if (paired_end_mapping_metadata.GetNumBestMappings() == 1) {

src/mapping_generator.h

+69 −64
Original line number Diff line number Diff line
@@ -65,7 +65,8 @@ class MappingGenerator { 
      uint32_t pair_index, const SequenceBatch &read_batch1,

      const SequenceBatch &read_batch2, const SequenceBatch &barcode_batch,

      const SequenceBatch &reference, std::vector<int> &best_mapping_indices,

      int force_mapq, PairedEndMappingMetadata &paired_end_mapping_metadata,

      std::mt19937 &generator, int force_mapq,

      PairedEndMappingMetadata &paired_end_mapping_metadata,

      std::vector<std::vector<MappingRecord>> &mappings_on_diff_ref_seqs);



 private:
@@ -278,7 +279,7 @@ void MappingGenerator<MappingRecord>::GenerateBestMappingsForPairedEndRead( 
    uint32_t pair_index, const SequenceBatch &read_batch1,

    const SequenceBatch &read_batch2, const SequenceBatch &barcode_batch,

    const SequenceBatch &reference, std::vector<int> &best_mapping_indices,

    int force_mapq,

    std::mt19937 &generator, int force_mapq,

    PairedEndMappingMetadata &paired_end_mapping_metadata,

    std::vector<std::vector<MappingRecord>> &mappings_on_diff_ref_seqs) {

  const int num_positive_candidates1 =
@@ -422,7 +423,7 @@ void MappingGenerator<MappingRecord>::GenerateBestMappingsForPairedEndRead( 
    // std::vector<int> best_mapping_indices(max_num_best_mappings_);

    std::iota(best_mapping_indices.begin(), best_mapping_indices.end(), 0);

    if (num_best_mappings > max_num_best_mappings_) {

      std::mt19937 generator(11);

      // std::mt19937 generator(11);

      for (int i = max_num_best_mappings_; i < num_best_mappings; ++i) {

        std::uniform_int_distribution<int> distribution(

            0, i);  // important: inclusive range
@@ -595,14 +596,16 @@ void MappingGenerator<MappingRecord>::ProcessBestMappingsForSingleEndRead( 
}



template <typename MappingRecord>

void MappingGenerator<MappingRecord>::GenerateBestMappingsForPairedEndReadOnOneDirection(

    Direction first_read_direction, uint32_t pair_index, int num_candidates1,

    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, int num_candidates2,

    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,

void MappingGenerator<MappingRecord>::

    GenerateBestMappingsForPairedEndReadOnOneDirection(

        Direction first_read_direction, uint32_t pair_index,

        int num_candidates1, 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,

        int num_candidates2, 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 std::vector<std::pair<int, uint64_t>> &mappings2,

        std::vector<std::pair<uint32_t, uint32_t>> &best_mappings,

        int &min_sum_errors, int &num_best_mappings, int &second_min_sum_errors,
@@ -708,13 +711,14 @@ void MappingGenerator<MappingRecord>::GenerateBestMappingsForPairedEndReadOnOneD 
}



template <typename MappingRecord>

void MappingGenerator<MappingRecord>::RecalibrateBestMappingsForPairedEndReadOnOneDirection(

void MappingGenerator<MappingRecord>::

    RecalibrateBestMappingsForPairedEndReadOnOneDirection(

        Direction first_read_direction, uint32_t pair_index, int min_sum_errors,

        int second_min_sum_errors, 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, int min_num_errors2,

    int num_best_mappings2, int second_min_num_errors2,

        const std::vector<std::pair<int, uint64_t>> &mappings1,

        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 std::vector<std::pair<int, uint64_t>> &mappings2,
@@ -820,7 +824,8 @@ void MappingGenerator<MappingRecord>::RecalibrateBestMappingsForPairedEndReadOnO 
}



template <typename MappingRecord>

void MappingGenerator<MappingRecord>::ProcessBestMappingsForPairedEndReadOnOneDirection(

void MappingGenerator<MappingRecord>::

    ProcessBestMappingsForPairedEndReadOnOneDirection(

        Direction first_read_direction, Direction second_read_direction,

        uint32_t pair_index, uint8_t mapq, int num_candidates1,

        uint32_t repetitive_seed_length1, int min_num_errors1,

CRA Git | Maintained and supported by SUSTech CRA and CCSE