1 #ifndef CODE_ParametersChimeric 2 #define CODE_ParametersChimeric 3 4 #include "IncludeDefine.h" 5 6 class Parameters; 7 8 class ParametersChimeric 9 {// 10 public: 11 uint segmentMin, junctionOverhangMin; //min chimeric donor/acceptor length 12 uint segmentReadGapMax; //max read gap for stitching chimeric windows 13 int scoreMin,scoreDropMax,scoreSeparation, scoreJunctionNonGTAG; //min chimeric score 14 uint mainSegmentMultNmax; 15 16 uint multimapScoreRange, multimapNmax, nonchimScoreDropMin; 17 18 vector<int> outJunctionFormat; 19 20 struct 21 { 22 vector <string> stringIn; 23 bool genomicN; 24 } filter; 25 26 struct 27 { 28 vector <string> type; 29 bool bam; 30 bool bamHardClip; 31 bool samOld; 32 bool junctions; 33 } out; 34 35 void initialize(Parameters *pPin); 36 37 private: 38 Parameters *pP; 39 }; 40 41 #endif