fastq_iterator.h

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#ifndef gamgee__fastq_iterator__guard
#define gamgee__fastq_iterator__guard

#include "fastq.h"

#include <memory>
#include <istream>

namespace gamgee {

class FastqIterator {
 public:

  FastqIterator();

  explicit FastqIterator(std::shared_ptr<std::istream>& in);

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

  FastqIterator(FastqIterator&&) = default;
  FastqIterator& operator=(FastqIterator&&) = default;

  bool operator==(const FastqIterator& rhs) const;

  bool operator!=(const FastqIterator& rhs) const;

  Fastq& operator*();

  Fastq& operator++();
  
 private:
  std::shared_ptr<std::istream> m_input_stream;         
  Fastq m_element;              
  bool m_is_fastq;              
  char m_eos_delim;             
  char m_bor_delim;             
  
  Fastq fetch_next_element();
  std::string parse_comment();
  std::string parse_seq();
  std::string parse_quals(uint32_t seq_length);
  const std::string parse_multiline();
  void skip_new_lines();
};

}  // end namespace gamgee

#endif // gamgee__fastq_iterator__guard