indexed_variant_iterator.h

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#ifndef gamgee__indexed_variant_iterator__guard
#define gamgee__indexed_variant_iterator__guard

#include "variant_iterator.h"

#include "../utils/hts_memory.h"

#include "htslib/vcf.h"

#include <memory>
#include <string>
#include <vector>

namespace gamgee {

class IndexedVariantIterator : public VariantIterator {
 public:

  static const std::vector<std::string> all_intervals;

  IndexedVariantIterator();

  IndexedVariantIterator(const std::shared_ptr<htsFile>& file_ptr,
                         const std::shared_ptr<hts_idx_t>& index_ptr,
                         const std::shared_ptr<bcf_hdr_t>& header_ptr,
                         const std::vector<std::string>& interval_list = all_intervals);

  IndexedVariantIterator(const IndexedVariantIterator& other) = delete;
  IndexedVariantIterator& operator=(const IndexedVariantIterator& other) = delete;

  IndexedVariantIterator(IndexedVariantIterator&& other) = default;
  IndexedVariantIterator& operator=(IndexedVariantIterator&& other) = default;

  bool operator!=(const IndexedVariantIterator& rhs);

 protected:
  void fetch_next_record() override;                                       

 private:
  std::shared_ptr<hts_idx_t> m_variant_index_ptr;                          
  std::vector<std::string> m_interval_list;                                
  std::vector<std::string>::const_iterator m_interval_iter;                
  std::unique_ptr<hts_itr_t, utils::HtsIteratorDeleter> m_index_iter_ptr;  
};

}

#endif  /* defined(gamgee__indexed_variant_iterator__guard) */