text: /*
  Part of Scallop Transcript Assembler
  (c) 2017 by  Mingfu Shao, Carl Kingsford, and Carnegie Mellon University.
  See LICENSE for licensing.
  */
  
  #ifndef __BRIDGE_H__
  #define __BRIDGE_H__
  
  #include <stdint.h>
  #include <string>
  
  using namespace std;
  
  class junction
  {
  public:
  	junction();
  	junction(int64_t _p);
  	junction(int64_t _p, int32_t _c);
  	junction(const junction &p);
  
  	bool operator<(const junction &x) const;
  
  public:
  	int32_t lpos;		// left position [left, right)
  	int32_t rpos;		// right position
  	int count;			// number of hits having this splice junction
  	char strand;		// strandness of this junction
  	int nm;				// total mismatch
  
  	int lexon;			// region index corresponds to lpos
  	int rexon;			// region index corresponds to rpos
  
  public:
  	int print(const string &chrm, int index) const;
  };
  
  bool junction_cmp_length(const junction &x, const junction &y);
  
  #endif
  