indexed_sam_reader.h

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#ifndef gamgee__indexed_sam_reader__guard
#define gamgee__indexed_sam_reader__guard

#include "indexed_sam_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 IndexedSamReader {
  public:

    IndexedSamReader(const std::string& filename, const std::vector<std::string>& interval_list) :
      m_sam_file_ptr {},
      m_sam_index_ptr {},
      m_sam_header_ptr {},
      m_interval_list {interval_list}
    {
      init_reader(filename);
    }

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

    IndexedSamReader(const IndexedSamReader& other) = delete;

    IndexedSamReader& operator=(IndexedSamReader& other) = delete;

    ITERATOR begin() {
      if (m_interval_list.empty())
        return ITERATOR{};
      else
        return ITERATOR{m_sam_file_ptr, m_sam_index_ptr, m_sam_header_ptr, m_interval_list};
    }

    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<hts_idx_t> m_sam_index_ptr;  
    std::shared_ptr<bam_hdr_t> m_sam_header_ptr; 
    std::vector<std::string> m_interval_list;    

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

      auto* index_ptr = sam_index_load(m_sam_file_ptr.get(), filename.c_str());
      if ( index_ptr == nullptr ) {
        throw IndexLoadException{filename};
      }
      m_sam_index_ptr = utils::make_shared_hts_index(index_ptr);

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

using IndexedSingleSamReader = IndexedSamReader<IndexedSamIterator>;

}

#endif