sam_iterator.h

Go to the documentation of this file.

#ifndef gamgee__sam_iterator__guard
#define gamgee__sam_iterator__guard

#include "sam.h"

#include "htslib/sam.h"

#include <memory>

namespace gamgee {

class SamIterator {
  public:

    SamIterator();

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

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

    SamIterator(SamIterator&&) = default;
    SamIterator& operator=(SamIterator&&) = default;
    
    bool operator!=(const SamIterator& rhs);

    Sam& operator*();

    Sam& operator++();

  private:
    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_ptr;    
    Sam m_sam_record;                            

    void fetch_next_record();                    
};

}  // end namespace gamgee

#endif // gamgee__sam_iterator__guard