sam_header.h

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#ifndef gamgee__sam_header__guard
#define gamgee__sam_header__guard

#include "htslib/sam.h"
#include "read_group.h"

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

namespace gamgee {

class SamHeader {
 public:
  explicit SamHeader() = default;                                   
  explicit SamHeader(const std::shared_ptr<bam_hdr_t>& header);     
  SamHeader(const SamHeader& other);                                
  SamHeader& operator=(const SamHeader& other);                     
  SamHeader(SamHeader&& other) = default;                           
  SamHeader& operator=(SamHeader&& other) = default;                
  uint32_t n_sequences() const {return m_header->n_targets;}        
  uint32_t sequence_length(const std::string& sequence_name) const; 
  uint32_t sequence_length(const uint32_t sequence_index) const { return m_header->target_len[sequence_index]; }                
  std::string sequence_name(const uint32_t sequence_index) const { return std::string(m_header->target_name[sequence_index]); } 
  std::vector<ReadGroup> read_groups() const;

 private:
  std::string header_text() const { return std::string(m_header->text, m_header->l_text); } 
  std::shared_ptr<bam_hdr_t> m_header;

  friend class SamWriter;
  friend class SamBuilder;
};

}
#endif // gamgee__sam_header__guard