Commit 157e5b15 authored by Haowen Zhang's avatar Haowen Zhang Committed by swiftgenomics
Browse files

Rename two funcs to supplement candidates.

parent e5377e79

src/candidate_processor.cc

+20 −18
Original line number Original line Diff line number Diff line
@@ -162,18 +162,18 @@ int CandidateProcessor::SupplementCandidates( 
      int negative_rescue_result = 0;

      int negative_rescue_result = 0;

      if (mate_positive_candidates->size() > 0) {

      if (mate_positive_candidates->size() > 0) {

        positive_rescue_result =

        positive_rescue_result =

            GenerateCandidatesFromRepetitiveReadWithMateInfo(

            GenerateCandidatesFromRepetitiveReadWithMateInfoOnOneStrand(

                error_threshold, index, *minimizers, *repetitive_seed_length,

                kNegative, search_range, error_threshold, index, *minimizers,

                *negative_hits, *augment_negative_candidates,

                *mate_positive_candidates, *repetitive_seed_length,

                *mate_positive_candidates, kNegative, search_range);

                *negative_hits, *augment_negative_candidates);

      }

      }





      if (mate_negative_candidates->size() > 0) {

      if (mate_negative_candidates->size() > 0) {

        negative_rescue_result =

        negative_rescue_result =

            GenerateCandidatesFromRepetitiveReadWithMateInfo(

            GenerateCandidatesFromRepetitiveReadWithMateInfoOnOneStrand(

                error_threshold, index, *minimizers, *repetitive_seed_length,

                kPositive, search_range, error_threshold, index, *minimizers,

                *positive_hits, *augment_positive_candidates,

                *mate_negative_candidates, *repetitive_seed_length,

                *mate_negative_candidates, kPositive, search_range);

                *positive_hits, *augment_positive_candidates);

      }

      }





      // If one of the strand did not supplement due to too many best candidate,

      // If one of the strand did not supplement due to too many best candidate,
@@ -262,13 +262,15 @@ void CandidateProcessor::ReduceCandidatesForPairedEndRead( 
      filtered_negative_candidates1, filtered_positive_candidates2);

      filtered_negative_candidates1, filtered_positive_candidates2);

}

}





int CandidateProcessor::GenerateCandidatesFromRepetitiveReadWithMateInfo(

int CandidateProcessor::

    int error_threshold, const Index &index,

    GenerateCandidatesFromRepetitiveReadWithMateInfoOnOneStrand(

    const std::vector<Minimizer> &minimizers, uint32_t &repetitive_seed_length,

        const Strand strand, uint32_t search_range, int error_threshold,

    std::vector<uint64_t> &hits, std::vector<Candidate> &candidates,

        const Index &index, const std::vector<Minimizer> &minimizers,

    const std::vector<Candidate> &mate_candidates, const Strand strand,

        const std::vector<Candidate> &mate_candidates,

    uint32_t search_range) const {

        uint32_t &repetitive_seed_length, std::vector<uint64_t> &hits,

  int max_seed_count = index.CollectSeedHitsFromRepetitiveReadWithMateInfo(

        std::vector<Candidate> &candidates) const {

  int max_seed_count =

      index.GenerateCandidatePositionsFromRepetitiveReadWithMateInfo(

          error_threshold, minimizers, repetitive_seed_length, hits,

          error_threshold, minimizers, repetitive_seed_length, hits,

          mate_candidates, strand, search_range,

          mate_candidates, strand, search_range,

          min_num_seeds_required_for_mapping_, max_seed_frequencies_[0]);

          min_num_seeds_required_for_mapping_, max_seed_frequencies_[0]);

src/candidate_processor.h

+5 −6
Original line number Original line Diff line number Diff line
@@ -46,13 +46,12 @@ class CandidateProcessor { 
                                     std::vector<uint64_t> &hits,

                                     std::vector<uint64_t> &hits,

                                     std::vector<Candidate> &candidates) const;

                                     std::vector<Candidate> &candidates) const;





  int GenerateCandidatesFromRepetitiveReadWithMateInfo(

  int GenerateCandidatesFromRepetitiveReadWithMateInfoOnOneStrand(

      int error_threshold, const Index &index,

      const Strand strand, uint32_t search_range, int error_threshold,

      const std::vector<Minimizer> &minimizers,

      const Index &index, const std::vector<Minimizer> &minimizers,

      const std::vector<Candidate> &mate_candidates,

      uint32_t &repetitive_seed_length, std::vector<uint64_t> &hits,

      uint32_t &repetitive_seed_length, std::vector<uint64_t> &hits,

      std::vector<Candidate> &candidates,

      std::vector<Candidate> &candidates) const;

      const std::vector<Candidate> &mate_candidates, const Strand strand,

      uint32_t search_range) const;





  void MergeCandidates(int error_threshold, std::vector<Candidate> &c1,

  void MergeCandidates(int error_threshold, std::vector<Candidate> &c1,

                       std::vector<Candidate> &c2,

                       std::vector<Candidate> &c2,

src/chromap.h

+1 −1
Original line number Original line Diff line number Diff line
@@ -29,7 +29,7 @@ 
#include "temp_mapping.h"

#include "temp_mapping.h"

#include "utils.h"

#include "utils.h"





#define CHROMAP_VERSION "0.2.3-r435"

#define CHROMAP_VERSION "0.2.3-r436"





namespace chromap {

namespace chromap {

src/index.cc

+1 −1
Original line number Original line Diff line number Diff line
@@ -459,7 +459,7 @@ int Index::GenerateCandidatePositions( 
  return repetitive_seed_count;

  return repetitive_seed_count;

}

}





int Index::CollectSeedHitsFromRepetitiveReadWithMateInfo(

int Index::GenerateCandidatePositionsFromRepetitiveReadWithMateInfo(

    int error_threshold, const std::vector<Minimizer> &minimizers,

    int error_threshold, const std::vector<Minimizer> &minimizers,

    uint32_t &repetitive_seed_length, std::vector<uint64_t> &hits,

    uint32_t &repetitive_seed_length, std::vector<uint64_t> &hits,

    const std::vector<Candidate> &mate_candidates, const Strand strand,

    const std::vector<Candidate> &mate_candidates, const Strand strand,

src/index.h

+5 −5
Original line number Original line Diff line number Diff line
@@ -72,11 +72,11 @@ class Index { 
      const CandidatePositionGeneratingConfig &generating_config,

      const CandidatePositionGeneratingConfig &generating_config,

      MappingMetadata &mapping_metadata) const;

      MappingMetadata &mapping_metadata) const;





  // Input a search range, for each best mate candidate, serach for minimizer

  // Input a search range, for each best mate candidate, serach for candidate

  // hits. Return the minimizer count of the best candidate if it finishes

  // positions for the read. Return the minimizer count of the best candidate if

  // normally. Or return a negative value if it stops early due to too many

  // it finishes normally. Or return a negative value if it stops early due to

  // candidates with low minimizer count.

  // too many candidates with low minimizer count.

  int CollectSeedHitsFromRepetitiveReadWithMateInfo(

  int GenerateCandidatePositionsFromRepetitiveReadWithMateInfo(

      int error_threshold, const std::vector<Minimizer> &minimizers,

      int error_threshold, const std::vector<Minimizer> &minimizers,

      uint32_t &repetitive_seed_length, std::vector<uint64_t> &hits,

      uint32_t &repetitive_seed_length, std::vector<uint64_t> &hits,

      const std::vector<Candidate> &mate_candidates, const Strand strand,

      const std::vector<Candidate> &mate_candidates, const Strand strand,

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