sam_reader.h

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#ifndef gamgee__sam_reader__guard
#define gamgee__sam_reader__guard

#include "sam_iterator.h"
#include "sam_pair_iterator.h"

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

#include "htslib/sam.h"

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

namespace gamgee {

template<class ITERATOR>
class SamReader {
  public:

    SamReader(const std::string& filename) :
      m_sam_file_ptr {},
      m_sam_header_ptr {}
    {
      init_reader(filename);
    }

    SamReader(const std::vector<std::string>& filenames) :
      m_sam_file_ptr {},
      m_sam_header_ptr {}
    {
      if (filenames.size() > 1)
        throw SingleInputException{"filenames", filenames.size()};
      if (!filenames.empty())
        init_reader(filenames.front());
    }

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

    SamReader(SamReader&&) = default;
    SamReader& operator=(SamReader&&) = default;

    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:
    std::shared_ptr<htsFile> m_sam_file_ptr;     
    std::shared_ptr<bam_hdr_t> m_sam_header_ptr; 

    void init_reader (const std::string& filename) {
      auto* file_ptr = sam_open(filename.empty() ? "-" : filename.c_str(), "r");
      if ( file_ptr == nullptr ) {
        throw FileOpenException{filename};
      }
      m_sam_file_ptr  = utils::make_shared_hts_file(file_ptr);

      auto* header_ptr = sam_hdr_read(file_ptr);
      if ( header_ptr == nullptr ) {
        throw HeaderReadException{filename};
      }
      m_sam_header_ptr = utils::make_shared_sam_header(header_ptr);
    }
};

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

}  // end of namespace

#endif /* defined(gamgee__sam_reader__guard) */