indexed_sam_iterator.h

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#ifndef gamgee__indexed_sam_iterator__guard
#define gamgee__indexed_sam_iterator__guard

#include "sam.h"

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

#include "htslib/sam.h"

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

namespace gamgee {

class IndexedSamIterator {
  public:
    IndexedSamIterator();

    IndexedSamIterator(const std::shared_ptr<htsFile>& sam_file_ptr, const std::shared_ptr<hts_idx_t>& sam_index_ptr,
        const std::shared_ptr<bam_hdr_t>& sam_header_ptr, const std::vector<std::string>& interval_list);

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

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

    bool operator!=(const IndexedSamIterator& rhs);

    Sam& operator*();

    Sam& operator++();

    const std::string& current_interval() const;

  private:
    std::shared_ptr<htsFile> m_sam_file_ptr;                
    std::shared_ptr<hts_idx_t> m_sam_index_ptr;             
    std::shared_ptr<bam_hdr_t> m_sam_header_ptr;            
    std::vector<std::string> m_interval_list;               
    std::vector<std::string>::iterator m_interval_iterator; 
    std::unique_ptr<hts_itr_t, utils::HtsIteratorDeleter> m_sam_itr_ptr; 
    std::shared_ptr<bam1_t> m_sam_record_ptr;               
    Sam m_sam_record;                                       

    void fetch_next_record();                               
};

}

#endif