sam.h

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#ifndef gamgee__sam__guard
#define gamgee__sam__guard

#include "sam_header.h"
#include "read_bases.h"
#include "base_quals.h"
#include "cigar.h"
#include "sam_tag.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& operator=(const Sam& other);

  Sam(Sam&& other) = default;

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

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

  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())); }   

  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_alignment_stop(const SamTag<std::string>& mate_cigar_tag) const ;       

  uint32_t mate_unclipped_start() const;                                                 

  uint32_t mate_unclipped_start(const SamTag<std::string>& mate_cigar_tag) const;        

  uint32_t mate_unclipped_stop() const ;                                                

  uint32_t mate_unclipped_stop(const SamTag<std::string>& mate_cigar_tag) const;        

  uint8_t mapping_qual() const { return uint8_t(m_body->core.qual); }

  int32_t insert_size() const { return m_body->core.isize; }

  // 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); } 
  void set_mapping_qual(const uint8_t mapq)            { m_body->core.qual = mapq;                } 
  void set_insert_size(const int32_t isize)        { m_body->core.isize = isize;              } 

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

  // getters for tagged values within the aux part of the data field
  SamTag<int32_t> integer_tag(const std::string& tag_name) const;    
  SamTag<double> double_tag(const std::string& tag_name) const;      
  SamTag<char> char_tag(const std::string& tag_name) const;          
  SamTag<std::string> string_tag(const std::string& tag_name) const; 

  // 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 mate_unmapped() const { return m_body->core.flag & BAM_FMUNMAP;        }   
  bool reverse() const { return m_body->core.flag & BAM_FREVERSE;       }         
  bool mate_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_mate_unmapped()     { m_body->core.flag |= BAM_FMUNMAP;         }
  void set_not_mate_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_mate_reverse()      { m_body->core.flag |= BAM_FMREVERSE;       }
  void set_not_mate_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; 
  friend class SamBuilder; 
};

}  // end of namespace

#endif /* defined(gamgee__sam__guard) */