variant.h

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#ifndef __gamgee__variant__
#define __gamgee__variant__

#include "variant_header.h"

#include "htslib/sam.h"

#include <string>
#include <memory>

namespace gamgee {

class Variant {
 public:
  Variant() = default;                                                                                      
  explicit Variant(const std::shared_ptr<bcf_hdr_t>& header, const std::shared_ptr<bcf1_t>& body) noexcept; 
  Variant(const Variant& other);                                                                            
  Variant(Variant&& other) noexcept;                                                                        
  Variant& operator=(const Variant& other);                                                                 
  Variant& operator=(Variant&& other) noexcept;                                                             

  VariantHeader header() const { return VariantHeader{m_header}; }

  uint32_t chromosome()      const {return uint32_t(m_body->rid);}      
  uint32_t alignment_start() const {return uint32_t(m_body->pos+1);}    
  uint32_t qual()            const {return uint32_t(m_body->qual);}     
  uint32_t n_samples()       const {return uint32_t(m_body->n_sample);} 
  uint32_t n_alleles()       const {return uint32_t(m_body->n_allele);} 

  std::vector<uint8_t> genotype_quals() const; 

 private:
  std::shared_ptr<bcf_hdr_t> m_header; 
  std::shared_ptr<bcf1_t> m_body;      

  friend class VariantWriter;
};

}  // end of namespace

#endif /* defined(__gamgee__variant__) */