Short parameter list for index construction.

  SequenceBatch reference;

  reference.InitializeLoading(index_parameters_.reference_file_path);

  uint32_t num_sequences = reference.LoadAllSequences();

  Index index(index_parameters_.kmer_size, index_parameters_.window_size,

              index_parameters_.num_threads,

              index_parameters_.index_output_file_path);

  Index index(index_parameters_);

  index.Construct(num_sequences, reference);

  index.Statistics(num_sequences, reference);

  index.Save();

#include "khash.h"

#include "mapping_metadata.h"

#include "index_parameters.h"

#include "sequence_batch.h"

#include "utils.h"

namespace chromap {

#define KHashFunctionForIndex(a) ((a) >> 1)

#define KHashEqForIndex(a, b) ((a) >> 1 == (b) >> 1)

KHASH_INIT(k64, uint64_t, uint64_t, 1, KHashFunctionForIndex, KHashEqForIndex);

  }

  // For index construction.

  Index(int kmer_size, int window_size, int num_threads,

        const std::string &index_file_path)

      : kmer_size_(kmer_size),

        window_size_(window_size),

        num_threads_(num_threads),

        index_file_path_(index_file_path) {

  Index(const IndexParameters &index_parameters)

      : kmer_size_(index_parameters.kmer_size),

        window_size_(index_parameters.window_size),

        num_threads_(index_parameters.num_threads),

        index_file_path_(index_parameters.index_output_file_path) {

    lookup_table_ = kh_init(k64);

  }

  }

 protected:

  int kmer_size_;

  int window_size_;

  int kmer_size_ = 0;

  int window_size_ = 0;

  // Number of threads to build the index, which is not used right now.

  int num_threads_;

  int num_threads_ = 1;

  const std::string index_file_path_;

  khash_t(k64) *lookup_table_ = NULL;

  khash_t(k64) *lookup_table_ = nullptr;

  std::vector<uint64_t> occurrence_table_;

};