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#ifndef STATS_DEF
#define STATS_DEF
#include "IncludeDefine.h"
#include "Transcript.h"
#include "Parameters.h"
class Stats {
public:
uint readN;//number of reads from the file
uint readBases;//number of input bases
// uint mateLmax[2], mateLmin[2];//mates' max and min length
uint mappedReadsU, mappedReadsM;
uint mappedBases, mappedMismatchesN, mappedInsN, mappedDelN, mappedInsL, mappedDelL;
double mappedPortion; //portion of the read length that has been mapped
uint splicesN[SJ_MOTIF_SIZE];//non-can,3*can,annotated
uint splicesNsjdb;
uint unmappedOther, unmappedShort, unmappedMismatch, unmappedMulti, unmappedAll;
uint chimericAll;
time_t timeStart, timeStartMap, timeFinishMap, timeLastReport, timeFinish;
Stats ();
void resetN();
void printShort(ostream*);
void transcriptStats(Transcript &T, uint Lread);
void addStats(Stats &S);
void progressReportHeader(ofstream &progressStream);
void progressReport(ofstream &progressStream) ;
void reportFinal(ofstream &streamOut);
void writeLines(ofstream &streamOut, const vector<int> outType, const string commStr, const string outStr);// write commented lines to text files with stats
void qualHistCalc(const uint64 imate, const char* qual, const uint64 len);
//void qualHistCalcSolo(const uint64 imate, const char* qual, const vector<uint32> stlen);
};
#endif
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