sam_builder.h

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#ifndef gamgee__sam_builder__guard
#define gamgee__sam_builder__guard

#include "sam.h"
#include "sam_builder_data_field.h"

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

namespace gamgee {

class SamBuilder {
 public:
  explicit SamBuilder(const SamHeader& header, const bool validate_on_build = true);                           
  explicit SamBuilder(const Sam& starting_read, const bool validate_on_build = true);                          
  explicit SamBuilder(const SamHeader& header, const Sam& starting_read, const bool validate_on_build = true); 

  // SamBuilders are moveable but not copyable, and use default destruction
  SamBuilder(SamBuilder&& other) = default;
  SamBuilder& operator=(SamBuilder&& other) = default;
  SamBuilder(const SamBuilder& other) = delete;
  SamBuilder& operator=(const SamBuilder& other) = delete;
  ~SamBuilder() = default;

  // Setters for data fields
  SamBuilder& set_name(const std::string& new_name);

  SamBuilder& set_cigar(const Cigar& new_cigar);
  SamBuilder& set_cigar(const std::vector<CigarElement>& new_cigar);
  SamBuilder& set_cigar(const std::initializer_list<CigarElement> new_cigar);
  SamBuilder& set_cigar(const std::string& new_cigar);

  SamBuilder& set_bases(const ReadBases& new_bases);
  SamBuilder& set_bases(const std::vector<Base>& new_bases);
  SamBuilder& set_bases(const std::initializer_list<Base> new_bases);
  SamBuilder& set_bases(const std::string& new_bases);

  SamBuilder& set_base_quals(const BaseQuals& new_base_quals);
  SamBuilder& set_base_quals(const std::vector<uint8_t>& new_base_quals);
  SamBuilder& set_base_quals(const std::initializer_list<uint8_t> new_base_quals);
  SamBuilder& set_base_quals(const std::initializer_list<int> new_base_quals);

  // Setters for core fields: these pass through to the implementations in Sam
  SamBuilder& set_chromosome(const uint32_t chr)              { m_core_read.set_chromosome(chr); return *this;              } 
  SamBuilder& set_alignment_start(const uint32_t start)       { m_core_read.set_alignment_start(start); return *this;       } 
  SamBuilder& set_mate_chromosome(const uint32_t mchr)        { m_core_read.set_mate_chromosome(mchr); return *this;        } 
  SamBuilder& set_mate_alignment_start(const uint32_t mstart) { m_core_read.set_mate_alignment_start(mstart); return *this; } 
  SamBuilder& set_paired()            { m_core_read.set_paired(); return *this;            }
  SamBuilder& set_not_paired()        { m_core_read.set_not_paired(); return *this;        }
  SamBuilder& set_unmapped()          { m_core_read.set_unmapped(); return *this;          }
  SamBuilder& set_not_unmapped()      { m_core_read.set_not_unmapped(); return *this;      }
  SamBuilder& set_mate_unmapped()     { m_core_read.set_mate_unmapped(); return *this;     }
  SamBuilder& set_not_mate_unmapped() { m_core_read.set_not_mate_unmapped(); return *this; }
  SamBuilder& set_reverse()           { m_core_read.set_reverse(); return *this;           }
  SamBuilder& set_not_reverse()       { m_core_read.set_not_reverse(); return *this;       }
  SamBuilder& set_mate_reverse()      { m_core_read.set_mate_reverse(); return *this;      }
  SamBuilder& set_not_mate_reverse()  { m_core_read.set_not_mate_reverse(); return *this;  }
  SamBuilder& set_first()             { m_core_read.set_first(); return *this;             }
  SamBuilder& set_not_first()         { m_core_read.set_not_first(); return *this;         }
  SamBuilder& set_last()              { m_core_read.set_last(); return *this;              }
  SamBuilder& set_not_last()          { m_core_read.set_not_last(); return *this;          }
  SamBuilder& set_secondary()         { m_core_read.set_secondary(); return *this;         }
  SamBuilder& set_not_secondary()     { m_core_read.set_not_secondary(); return *this;     }
  SamBuilder& set_fail()              { m_core_read.set_fail(); return *this;              }
  SamBuilder& set_not_fail()          { m_core_read.set_not_fail(); return *this;          }
  SamBuilder& set_duplicate()         { m_core_read.set_duplicate(); return *this;         }
  SamBuilder& set_not_duplicate()     { m_core_read.set_not_duplicate(); return *this;     }
  SamBuilder& set_supplementary()     { m_core_read.set_supplementary(); return *this;     }
  SamBuilder& set_not_supplementary() { m_core_read.set_not_supplementary(); return *this; }

  Sam build() const;    
  Sam one_time_build(); 

 private:
  Sam m_core_read;   
  SamBuilderDataField m_name;       
  SamBuilderDataField m_cigar;      
  SamBuilderDataField m_bases;      
  SamBuilderDataField m_base_quals; 
  SamBuilderDataField m_tags;       
  bool m_validate_on_build;         

  void validate() const;                    
  void build_data_array(bam1_t* sam) const; 
};

}


#endif /* gamgee__sam_builder__guard */