Commit 5cab2035 authored by Haowen Zhang's avatar Haowen Zhang Committed by swiftgenomics
Browse files

Revise a func for candidate supplement.

parent 157e5b15

src/candidate_processor.cc

+4 −4
Original line number Original line Diff line number Diff line
@@ -270,10 +270,10 @@ int CandidateProcessor:: 
        uint32_t &repetitive_seed_length, std::vector<uint64_t> &hits,

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

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

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

  int max_seed_count =

  int max_seed_count =

      index.GenerateCandidatePositionsFromRepetitiveReadWithMateInfo(

      index.GenerateCandidatePositionsFromRepetitiveReadWithMateInfoOnOneStrand(

          error_threshold, minimizers, repetitive_seed_length, hits,

          strand, search_range, min_num_seeds_required_for_mapping_,

          mate_candidates, strand, search_range,

          max_seed_frequencies_[0], error_threshold, minimizers,

          min_num_seeds_required_for_mapping_, max_seed_frequencies_[0]);

          mate_candidates, repetitive_seed_length, hits);





  GenerateCandidatesOnOneStrand(error_threshold, /*num_seeds_required=*/1,

  GenerateCandidatesOnOneStrand(error_threshold, /*num_seeds_required=*/1,

                                minimizers.size(), hits, candidates);

                                minimizers.size(), hits, candidates);

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-r436"

#define CHROMAP_VERSION "0.2.3-r437"





namespace chromap {

namespace chromap {

src/index.cc

+5 −5
Original line number Original line Diff line number Diff line
@@ -459,12 +459,12 @@ int Index::GenerateCandidatePositions( 
  return repetitive_seed_count;

  return repetitive_seed_count;

}

}





int Index::GenerateCandidatePositionsFromRepetitiveReadWithMateInfo(

int Index::GenerateCandidatePositionsFromRepetitiveReadWithMateInfoOnOneStrand(

    const Strand strand, uint32_t search_range,

    int min_num_seeds_required_for_mapping, int max_seed_frequency0,

    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,

    const std::vector<Candidate> &mate_candidates,

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

    uint32_t &repetitive_seed_length, std::vector<uint64_t> &hits) const {

    uint32_t search_range, int min_num_seeds_required_for_mapping,

    int max_seed_frequency0) const {

  const uint32_t mate_candidates_size = mate_candidates.size();

  const uint32_t mate_candidates_size = mate_candidates.size();





  int max_minimizer_count = 0;

  int max_minimizer_count = 0;

src/index.h

+5 −5
Original line number Original line Diff line number Diff line
@@ -76,12 +76,12 @@ class Index { 
  // positions for the read. Return the minimizer count of the best candidate if

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

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

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

  // too many candidates with low minimizer count.

  // too many candidates with low minimizer count.

  int GenerateCandidatePositionsFromRepetitiveReadWithMateInfo(

  int GenerateCandidatePositionsFromRepetitiveReadWithMateInfoOnOneStrand(

      const Strand strand, uint32_t search_range,

      int min_num_seeds_required_for_mapping, int max_seed_frequency0,

      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,

      const std::vector<Candidate> &mate_candidates,

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

      uint32_t &repetitive_seed_length, std::vector<uint64_t> &hits) const;

      uint32_t search_range, int min_num_seeds_required_for_mapping,

      int max_seed_frequency0) const;





  int GetKmerSize() const { return kmer_size_; }

  int GetKmerSize() const { return kmer_size_; }

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