sam.h

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#ifndef __gamgee__sam__
#define __gamgee__sam__

#include "sam_header.h"
#include "read_bases.h"
#include "base_quals.h"
#include "cigar.h"

#include "htslib/sam.h"

#include <string>
#include <memory>

namespace gamgee {

class Sam {
 public:
  Sam() = default;                                                                                      
  explicit Sam(const std::shared_ptr<bam_hdr_t>& header, const std::shared_ptr<bam1_t>& body) noexcept; 
  Sam(const Sam& other);                                                                                
  Sam(Sam&& other) noexcept;                                                                            
  Sam& operator=(const Sam& other);                                                                     
  Sam& operator=(Sam&& other) noexcept;                                                                 

  SamHeader header() { return SamHeader{m_header}; }

  // getters for non-variable length fields (things outside of the data member)
  uint32_t chromosome()           const { return uint32_t(m_body->core.tid);     }       
  uint32_t alignment_start()      const { return uint32_t(m_body->core.pos+1);   }       
  uint32_t alignment_stop()       const { return uint32_t(bam_endpos(m_body.get())+1); } 
  uint32_t unclipped_start()      const ;
  uint32_t unclipped_stop()       const ;
  uint32_t mate_chromosome()      const { return uint32_t(m_body->core.mtid);    }       
  uint32_t mate_alignment_start() const { return uint32_t(m_body->core.mpos+1);  }       
  uint32_t mate_alignment_stop()  const ;                                                
  uint32_t mate_unclipped_start() const { return alignment_start();              }       
  uint32_t mate_unclipped_stop()  const ;                                                

  // modify non-variable length fields (things outside of the data member)
  void set_chromosome(const uint32_t chr)              { m_body->core.tid  = int32_t(chr);        } 
  void set_alignment_start(const uint32_t start)       { m_body->core.pos  = int32_t(start-1);    } 
  void set_mate_chromosome(const uint32_t mchr)        { m_body->core.mtid = int32_t(mchr);       } 
  void set_mate_alignment_start(const uint32_t mstart) { m_body->core.mpos = int32_t(mstart - 1); } 

  // getters for fields inside the data field
  std::string name()     const { return std::string{bam_get_qname(m_body.get())}; } 
  ReadBases bases()      const { return ReadBases{m_body}; }                        
  BaseQuals base_quals() const { return BaseQuals{m_body}; }                        
  Cigar cigar()          const { return Cigar{m_body}; }                            

  // getters for flags 
  bool paired()          const { return m_body->core.flag & BAM_FPAIRED;        } 
  bool properly_paired() const { return m_body->core.flag & BAM_FPROPER_PAIR;   } 
  bool unmapped()        const { return m_body->core.flag & BAM_FUNMAP;         } 
  bool next_unmapped()   const { return m_body->core.flag & BAM_FMUNMAP;        } 
  bool reverse()         const { return m_body->core.flag & BAM_FREVERSE;       } 
  bool next_reverse()    const { return m_body->core.flag & BAM_FMREVERSE;      } 
  bool first()           const { return m_body->core.flag & BAM_FREAD1;         } 
  bool last()            const { return m_body->core.flag & BAM_FREAD2;         } 
  bool secondary()       const { return m_body->core.flag & BAM_FSECONDARY;     } 
  bool fail()            const { return m_body->core.flag & BAM_FQCFAIL;        } 
  bool duplicate()       const { return m_body->core.flag & BAM_FDUP;           } 
  bool supplementary()   const { return m_body->core.flag & BAM_FSUPPLEMENTARY; } 

  // modify flags
  void set_paired()            { m_body->core.flag |= BAM_FPAIRED;         } 
  void set_not_paired()        { m_body->core.flag &= ~BAM_FPAIRED;        }
  void set_unmapped()          { m_body->core.flag |= BAM_FUNMAP;          }
  void set_not_unmapped()      { m_body->core.flag &= ~BAM_FUNMAP;         }
  void set_next_unmapped()     { m_body->core.flag |= BAM_FMUNMAP;         }
  void set_not_next_unmapped() { m_body->core.flag &= ~BAM_FMUNMAP;        }
  void set_reverse()           { m_body->core.flag |= BAM_FREVERSE;        }
  void set_not_reverse()       { m_body->core.flag &= ~BAM_FREVERSE;       }
  void set_next_reverse()      { m_body->core.flag |= BAM_FMREVERSE;       }
  void set_not_next_reverse()  { m_body->core.flag &= ~BAM_FMREVERSE;      }
  void set_first()             { m_body->core.flag |= BAM_FREAD1;          }
  void set_not_first()         { m_body->core.flag &= ~BAM_FREAD1;         }
  void set_last()              { m_body->core.flag |= BAM_FREAD2;          }
  void set_not_last()          { m_body->core.flag &= ~BAM_FREAD2;         }
  void set_secondary()         { m_body->core.flag |= BAM_FSECONDARY;      }
  void set_not_secondary()     { m_body->core.flag &= ~BAM_FSECONDARY;     }
  void set_fail()              { m_body->core.flag |= BAM_FQCFAIL;         }
  void set_not_fail()          { m_body->core.flag &= ~BAM_FQCFAIL;        }
  void set_duplicate()         { m_body->core.flag |= BAM_FDUP;            }
  void set_not_duplicate()     { m_body->core.flag &= ~BAM_FDUP;           }
  void set_supplementary()     { m_body->core.flag |= BAM_FSUPPLEMENTARY;  }
  void set_not_supplementary() { m_body->core.flag &= ~BAM_FSUPPLEMENTARY; }

  bool empty() const { return m_body == nullptr; } 

 private:
  std::shared_ptr<bam_hdr_t> m_header; 
  std::shared_ptr<bam1_t> m_body;      

  friend class SamWriter; 
};

}  // end of namespace

#endif /* defined(__gamgee__sam__) */