indexed_variant_reader.h

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#ifndef gamgee__indexed_variant_reader__guard
#define gamgee__indexed_variant_reader__guard

#include "indexed_variant_iterator.h"

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

#include "htslib/vcf.h"

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

namespace gamgee {

template<class ITERATOR>
class IndexedVariantReader {
 public:

  IndexedVariantReader(const std::string& filename, const std::vector<std::string>& interval_list) :
    m_variant_file_ptr {},
    m_variant_index_ptr {},
    m_variant_header_ptr {},
    m_interval_list { interval_list }
  {
    init_reader(filename);
  }

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

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

  ITERATOR begin() const {
    return ITERATOR{ m_variant_file_ptr, m_variant_index_ptr, m_variant_header_ptr, m_interval_list };
  }

  ITERATOR end() const {
    return ITERATOR{};
  }

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

 private:
  std::shared_ptr<vcfFile> m_variant_file_ptr;        
  std::shared_ptr<hts_idx_t> m_variant_index_ptr;     
  std::shared_ptr<bcf_hdr_t> m_variant_header_ptr;    
  std::vector<std::string> m_interval_list;           

  void init_reader(const std::string& filename) {
    // Need to check raw pointers for null before wrapping them in a shared_ptr to avoid a segfault
    // during destruction if an exception is thrown

    auto* variant_file_ptr = bcf_open(filename.c_str(), "r");
    if ( variant_file_ptr == nullptr ) {
      throw FileOpenException{filename};
    }
    m_variant_file_ptr = utils::make_shared_hts_file(variant_file_ptr);

    auto* index_file_ptr = bcf_index_load(filename.c_str());
    if ( index_file_ptr == nullptr ) {
      throw IndexLoadException{filename};
    }
    m_variant_index_ptr = utils::make_shared_hts_index(index_file_ptr);

    auto* header_ptr = bcf_hdr_read(m_variant_file_ptr.get());
    if ( header_ptr == nullptr ) {
      throw HeaderReadException{filename};
    }
    m_variant_header_ptr = utils::make_shared_variant_header(header_ptr);
  }
};

}

#endif  /* defined(gamgee__indexed_variant_reader__guard) */