Make alignment related functions free.

  // Supportive functions

  void ConstructIndex();

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

                               const int read_length,

                               int *mapping_end_location);

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

                                          const int read_length,

                                          int *mapping_end_location,

                                          int *read_mapping_length);

  int BandedAlignPatternToTextWithDropOffFrom3End(const char *pattern,

                                                  const char *text,

                                                  const int read_length,

                                                  int *mapping_end_position,

                                                  int *read_mapping_length);

  void BandedAlign4PatternsToText(const char **patterns, const char *text,

                                  int read_length,

                                  int32_t *mapping_edit_distances,

                                  int32_t *mapping_end_positions);

  void BandedAlign8PatternsToText(const char **patterns, const char *text,

                                  int read_length,

                                  int16_t *mapping_edit_distances,

                                  int16_t *mapping_end_positions);

  void BandedTraceback(int min_num_errors, const char *pattern,

                       const char *text, const int read_length,

                       int *mapping_start_position);

  void BandedTracebackToEnd(int min_num_errors, const char *pattern,

                            const char *text, const int read_length,

                            int *mapping_end_position);

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

                            const int read_length);

  size_t FindBestMappingIndexFromDuplicates(

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