sam_pair_iterator.h

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#ifndef gamgee__sam_pair_iterator__guard
#define gamgee__sam_pair_iterator__guard

#include "sam.h"

#include "htslib/sam.h"

#include <fstream>
#include <queue>
#include <memory>

namespace gamgee {

class SamPairIterator {
  public:

    SamPairIterator();

    SamPairIterator(const std::shared_ptr<htsFile>& sam_file_ptr, const std::shared_ptr<bam_hdr_t>& sam_header_ptr);

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

    SamPairIterator(SamPairIterator&& other) = default;
    SamPairIterator& operator=(SamPairIterator&& other) = default;
    
    bool operator!=(const SamPairIterator& rhs);

    std::pair<Sam,Sam> operator*();

    std::pair<Sam,Sam> operator++();

  private:
    using SamPtrQueue = std::queue<std::shared_ptr<bam1_t>>;

    SamPtrQueue m_supp_alignments;                     
    std::shared_ptr<htsFile> m_sam_file_ptr;           
    std::shared_ptr<bam_hdr_t> m_sam_header_ptr; 
    std::shared_ptr<bam1_t> m_sam_record_ptr1;         
    std::shared_ptr<bam1_t> m_sam_record_ptr2;         
    std::pair<Sam,Sam> m_sam_records;                  

    std::pair<Sam,Sam> fetch_next_pair();              
    bool read_sam(std::shared_ptr<bam1_t>& record_ptr);                 
    Sam make_sam(std::shared_ptr<bam1_t>& record_ptr);                  
    Sam next_primary_alignment(std::shared_ptr<bam1_t>& record_ptr);
    std::pair<Sam,Sam> next_supplementary_alignment();
};

}  // end namespace gamgee

#endif // gamgee__sam_pair_iterator__guard