Removed unused function declarations.

  // Supportive functions

  void ConstructIndex();

  int BandedAlignPatternToText(const char *pattern, const char *text,

                               const int read_length,

                               int *mapping_end_location);

      std::vector<std::pair<int, uint64_t> > &mappings, int &min_num_errors,

      int &num_best_mappings, int &second_min_num_errors,

      int &num_second_best_mappings);

  void VerifyCandidatesOnOneDirection(

      Direction candidate_direction, const SequenceBatch &read_batch,

      uint32_t read_index, const SequenceBatch &reference,

      std::vector<int> &split_sites, int &min_num_errors,

      int &num_best_mappings, int &second_min_num_errors,

      int &num_second_best_mappings);

  void VerifyCandidates(const SequenceBatch &read_batch, uint32_t read_index,

                        const SequenceBatch &reference,

                        MappingMetadata &mapping_metadata);

  void GenerateMDTag(const char *pattern, const char *text,

                     int mapping_start_position, int n_cigar,

                     const uint32_t *cigar, int &NM, std::string &MD_tag);

  void AllocateMultiMappings(uint32_t num_reference_sequences);

  void RemovePCRDuplicate(uint32_t num_reference_sequences);

  uint32_t MoveMappingsInBuffersToMappingContainer(

      uint32_t num_reference_sequences,

      std::vector<std::vector<std::vector<MappingRecord> > >

          &mappings_on_diff_ref_seqs_for_diff_threads_for_saving);

  void OutputBarcodeStatistics();

  void OutputMappingStatistics();

  void OutputMappingStatistics(

      uint32_t num_reference_sequences,

      const std::vector<std::vector<MappingRecord> > &uni_mappings,

      const std::vector<std::vector<MappingRecord> > &multi_mappings);

  uint8_t GetMAPQForSingleEndRead(

      int error_threshold, int num_candidates, uint32_t repetitive_seed_length,

      uint16_t alignment_length, int min_num_errors, int num_best_mappings,

      int second_min_num_errors, int num_second_best_mappings,

      int max_num_error_difference, int read_length);

  uint8_t GetMAPQForPairedEndRead(

      int num_positive_candidates, int num_negative_candidates,

      uint32_t repetitive_seed_length1, uint32_t repetitive_seed_length2,

      int second_min_num_errors2, int num_second_best_mappings1,

      int num_second_best_mappings2, int read1_length, int read2_length,

      int force_mapq, uint8_t &mapq1, uint8_t &mapq2);

  void SortOutputMappings(uint32_t num_reference_sequences,

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

  void BuildAugmentedTree(uint32_t ref_id);

  uint32_t GetNumOverlappedMappings(uint32_t ref_id,

                                    const MappingRecord &mapping);

  void LoadBarcodeWhitelist();

  void ComputeBarcodeAbundance(uint64_t max_num_sample_barcodes);

  void UpdateBarcodeAbundance(uint32_t num_loaded_barcodes,

                              const SequenceBatch &barcode_batch);

  bool CorrectBarcodeAt(uint32_t barcode_index, SequenceBatch &barcode_batch,

                        uint64_t &num_barcode_in_whitelist,

                        uint64_t &num_corrected_barcode);

  void BuildAugmentedTreeForPeaks(uint32_t ref_id);

  void OutputTempMappings(

      uint32_t num_reference_sequences,

      const MappingProcessor<MappingRecord> &mapping_processor);

  void OutputMappings(uint32_t num_reference_sequences,

                      const SequenceBatch &reference,

                      const std::vector<std::vector<MappingRecord> > &mappings);

  int AdjustGapBeginning(Direction mapping_direction, const char *ref,

                         const char *read, int *gap_beginning, int read_end,

                         int ref_start_position, int ref_end_position,

                         int *n_cigar, uint32_t **cigar);

  void GetRefStartEndPositionForReadFromMapping(

      Direction mapping_direction, const std::pair<int, uint64_t> &mapping,

      const char *read, int read_length, int in_split_site,

      const SequenceBatch &reference, uint32_t *ref_start_position,

      uint32_t *ref_end_position, int *n_cigar, uint32_t **cigar, int *NM,

      std::string &MD_TAG);

  void GenerateCustomizedRidRank(const std::string rid_order_path,

                                 const SequenceBatch &reference,

                                 std::vector<int> &rid_rank);

  void RerankCandidatesRid(std::vector<Candidate> &candidates);

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

 private: