5174 CPrediction* store_merge_prediction(GVec<int>& alltr,GPVec<CMTransfrag>& mgt,GVec<int>& path,  in store_merge_prediction()  argument
5190 	for(int i=0;i<alltr.Count();i++) {  in store_merge_prediction()
5191 		int a=alltr[i];  in store_merge_prediction()
5192 		cov+=mgt[alltr[i]]->transfrag->abundance;  in store_merge_prediction()
5194 		mgt[alltr[i]]->transfrag->abundance=0;  in store_merge_prediction()
5195 …if(enableNames || (alltr.Count()==1 && mgt[alltr[0]]->transfrag->real)) for(int j=0;j<mgt[a]->read…  in store_merge_prediction()
5252 CPrediction* store_merge_prediction(float cov,GVec<int>& alltr,GPVec<CMTransfrag>& mgt,GVec<int>& p…  in store_merge_prediction()  argument
5268 	if(enableNames) for(int i=0;i<alltr.Count();i++) {  in store_merge_prediction()
5269 		int a=alltr[i];  in store_merge_prediction()
5548 		GPVec<CGraphnode>& no2gnode,int gno,GIntHash<int>& gpos,GVec<int>& alltr,float &cov){  in add_transfrag_to_path()  argument
5558 		alltr.Add(t);  in add_transfrag_to_path()
5573 …				add_transfrag_to_path(tj,tforlater,ntforlater,mgt,pathpat,min,max,no2gnode,gno,gpos,alltr,cov);  in add_transfrag_to_path()
5589 …				add_transfrag_to_path(tj,tforlater,ntforlater,mgt,pathpat,min,max,no2gnode,gno,gpos,alltr,cov);  in add_transfrag_to_path()
5660 			GVec<int> alltr(1,t); // all transfrags used in creating path  in merge_transfrags()  local
5669 …CPrediction *p=store_merge_prediction(mgt[t]->transfrag->abundance,alltr,mgt,mgt[t]->transfrag->no…  in merge_transfrags()
5703 		GVec<int> alltr(1,t1);  in merge_transfrags()  local
5723 				alltr.Add(t2);  in merge_transfrags()
5726 				add_transfrag_to_path(t2,tforlater,ntforlater,mgt,pathpat,min,max,no2gnode,gno,gpos,alltr,cov);  in merge_transfrags()
5742 			if(alltr.Count()==1) printpath=mgt[t1]->transfrag->nodes; // only initial transfrag is in path  in merge_transfrags()
5744 				for(int i=0;i<alltr.Count();i++) {  in merge_transfrags()
5745 					int t=alltr[i];  in merge_transfrags()
5766 …CPrediction *p=store_merge_prediction(cov,alltr,mgt,printpath,no2gnode,strand,geneno,first,readlis…  in merge_transfrags()
10408 bool transcript_cont_path(GVec<int>& path,CTransfrag *transfrag, int &ni,GVec<int>& alltr,int t) {  in transcript_cont_path()  argument
10425 		alltr.Add(t);  in transcript_cont_path()
10432 void collect_path(GPVec<CMTransfrag>& mgt,GVec<int>& alltr,GVec<int>& path,GPVec<CGraphnode>& no2gn…  in collect_path()  argument
10448 				if(mgt[t]->transfrag->real && transcript_cont_path(path,mgt[t]->transfrag,ni,alltr,t)) {  in collect_path()
10453 …mgt[t]->transfrag->abundance>maxabund && transcript_cont_path(path,mgt[t]->transfrag,ni,alltr,t)) {  in collect_path()
10459 			else transcript_cont_path(path,mgt[t]->transfrag,ni,alltr,t);  in collect_path()
10465 	alltr.Add(maxt);  in collect_path()