reference_block_splitting_variant_iterator.h

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#ifndef __gamgee__reference_block_splitting_variant_iterator__
#define __gamgee__reference_block_splitting_variant_iterator__

#include "variant.h"
#include "multiple_variant_iterator.h"

#include <list>

namespace gamgee {

class ReferenceBlockSplittingVariantIterator : public MultipleVariantIterator {
 public:

  ReferenceBlockSplittingVariantIterator() = default;

  ReferenceBlockSplittingVariantIterator(const std::vector<std::shared_ptr<htsFile>>& variant_files, const std::vector<std::shared_ptr<bcf_hdr_t>>& variant_headers);

  ReferenceBlockSplittingVariantIterator(ReferenceBlockSplittingVariantIterator&&) = default;
  ReferenceBlockSplittingVariantIterator& operator=(ReferenceBlockSplittingVariantIterator&&) = default;

  ReferenceBlockSplittingVariantIterator(const ReferenceBlockSplittingVariantIterator&) = delete;
  ReferenceBlockSplittingVariantIterator& operator=(const ReferenceBlockSplittingVariantIterator&) = delete;

  bool operator!=(const ReferenceBlockSplittingVariantIterator& rhs);

  std::vector<VariantIndexPair>& operator*();

  std::vector<VariantIndexPair>& operator++();

 private:
  // fetches the next reference-block-split Variant vector
  // calls populate_pending() and populate_split_variants() as needed
  void fetch_next_split_vector();

  // populates the list of pending variants from the incoming vector of pre-split reference-block variants
  inline void populate_pending();

  // populates the vector of split variants from the list of pending variants, modifying the pending list as well
  inline void populate_split_variants();

  // holds the incoming reference-block variants before and during split operations
  std::vector<VariantIndexPair> m_pending_variants;

  // caches next reference-block-split Variant vector
  std::vector<VariantIndexPair> m_split_variants;

  unsigned int m_pending_chrom = UINT_MAX;
  unsigned int m_pending_start = UINT_MAX;
  unsigned int m_pending_min_end = UINT_MAX;
};

}  // end namespace gamgee

#endif  // __gamgee__reference_block_splitting_variant_iterator__