sam_reader.h

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#ifndef gamgee__sam_reader__
#define gamgee__sam_reader__

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

#include "htslib/sam.h"

#include <string>
#include <iostream>
#include <fstream>
#include <memory>


namespace gamgee {

template<class ITERATOR>
class SamReader {
  public:

    SamReader(const std::string& filename) :
      m_sam_file_ptr {sam_open(filename.empty() ? "-" : filename.c_str(), "r")},
      m_sam_header_ptr { utils::make_shared_sam_header(sam_hdr_read(m_sam_file_ptr)) }
    {}

    SamReader(SamReader&& other) :
      m_sam_file_ptr {std::move(other.m_sam_file_ptr)},
      m_sam_header_ptr {std::move(other.m_sam_header_ptr)}
    {}

    ~SamReader() {
      sam_close(m_sam_file_ptr);
    }

    SamReader(const SamReader&) = delete;

    ITERATOR begin() {
      return ITERATOR{m_sam_file_ptr, m_sam_header_ptr};
    }

    ITERATOR end() {
      return ITERATOR{};
    }

    inline SamHeader header() { return SamHeader{m_sam_header_ptr}; }

  private:
    samFile* m_sam_file_ptr;                           
    const std::shared_ptr<bam_hdr_t> m_sam_header_ptr; 
};

using SingleSamReader = SamReader<SamIterator>;
using PairSamReader = SamReader<SamPairIterator>;

}  // end of namespace

#endif /* defined(__gamgee__sam_iterator__) */