cigar.h

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#ifndef gamgee__cigar__guard
#define gamgee__cigar__guard

#include "htslib/sam.h"

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

namespace gamgee {

enum class CigarOperator { M, I, D, N, S, H, P, EQ, X, B };

using CigarElement = uint32_t;

class Cigar {
 public:
  explicit Cigar(const std::shared_ptr<bam1_t>& sam_record);
  Cigar(const Cigar& other);
  Cigar(Cigar&& other) = default;
  Cigar& operator=(const Cigar& other);
  Cigar& operator=(Cigar&& other) = default;
  ~Cigar() = default; 

  CigarElement operator[](const uint32_t index) const;       
  CigarElement& operator[](const uint32_t index);            
  uint32_t size() const { return m_num_cigar_elements; } 
  bool operator==(const Cigar& other) const;  
  bool operator!=(const Cigar& other) const;  
  std::string to_string() const;  

  inline static CigarOperator cigar_op(const CigarElement cigar_element) {
    return static_cast<CigarOperator>(bam_cigar_op(cigar_element));
  }

  inline static uint32_t cigar_oplen(const CigarElement cigar_element) {
    return bam_cigar_oplen(cigar_element);
  }

  inline static CigarElement make_cigar_element(const uint32_t oplen, const CigarOperator op) {
    return (oplen << BAM_CIGAR_SHIFT) | static_cast<uint32_t>(op);
  }
  
  static const std::vector<int8_t> cigar_op_parse_table;

  static CigarElement parse_next_cigar_element (std::stringstream& cigar_stream);

  inline static bool consumes_read_bases(const CigarOperator op) {return bam_cigar_type(static_cast<int8_t>(op))&1;}      
  inline static bool consumes_reference_bases(const CigarOperator op) {return bam_cigar_type(static_cast<int8_t>(op))&2;} 



 private:
  std::shared_ptr<bam1_t> m_sam_record;   
  uint32_t* m_cigar;                      
  uint32_t m_num_cigar_elements;          

  static const char cigar_ops_as_chars[]; 

  friend class SamBuilder; 
};

}

#endif /* gamgee__cigar__guard */