variant_reader.h

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#ifndef gamgee__variant_reader__
#define gamgee__variant_reader__

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

#include "htslib/vcf.h"

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


namespace gamgee {

template<class ITERATOR>
class VariantReader {
 public:

  VariantReader(const std::string& filename) :
    m_variant_file_ptr {bcf_open(filename.empty() ? "-" : filename.c_str(), "r")},
    m_variant_header_ptr { utils::make_shared_variant_header(bcf_hdr_read(m_variant_file_ptr)) }
  {}

  VariantReader(VariantReader&& other) :
    m_variant_file_ptr {std::move(other.m_variant_file_ptr)},
    m_variant_header_ptr {std::move(other.m_variant_header_ptr)}
  {}

  ~VariantReader() {
    bcf_close(m_variant_file_ptr);
  }

  VariantReader(const VariantReader&) = delete;

  ITERATOR begin() {
    return ITERATOR{m_variant_file_ptr, m_variant_header_ptr};
  }

  ITERATOR end() {
    return ITERATOR{};
  }

  inline VariantHeader header() { return VariantHeader{m_variant_header_ptr}; }

 private:
  vcfFile* m_variant_file_ptr;                           
  const std::shared_ptr<bcf_hdr_t> m_variant_header_ptr; 
};

using SingleVariantReader = VariantReader<VariantIterator>;

}  // end of namespace

#endif /* defined(__gamgee__variant_iterator__) */