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