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#include "Stats.h"
#include "TimeFunctions.h"
void Stats::resetN() {//zero all counters
readN = 0; readBases = 0;
mappedMismatchesN = 0; mappedInsN = 0; mappedDelN = 0; mappedInsL = 0; mappedDelL = 0; mappedBases = 0; mappedPortion = 0;
mappedReadsU = 0; mappedReadsM = 0;
unmappedOther = 0; unmappedShort = 0; unmappedMismatch = 0; unmappedMulti = 0; unmappedAll = 0;
chimericAll = 0;
splicesNsjdb=0;
for (uint ii=0; ii<SJ_MOTIF_SIZE; ii++) {
splicesN[ii]=0;
};
};
Stats::Stats() {//constructor
resetN();
timeLastReport=0;
};
void Stats::addStats(Stats &S) {//add S to Stats
readN += S.readN; readBases += S.readBases;
mappedMismatchesN += S.mappedMismatchesN; mappedInsN += S.mappedInsN; mappedDelN += S.mappedDelN;
mappedInsL += S.mappedInsL; mappedDelL += S.mappedDelL; mappedBases += S.mappedBases; mappedPortion += S.mappedPortion;
mappedReadsU += S.mappedReadsU; mappedReadsM += S.mappedReadsM;
unmappedOther += S.unmappedOther; unmappedShort += S.unmappedShort; unmappedMismatch += S.unmappedMismatch; unmappedMulti += S.unmappedMulti; unmappedAll += S.unmappedAll;
chimericAll += S.chimericAll;
splicesNsjdb += S.splicesNsjdb;
for (uint ii=0; ii<SJ_MOTIF_SIZE; ii++) {
splicesN[ii] +=S.splicesN[ii];
};
};
void Stats::transcriptStats(Transcript &T, uint Lread) {
mappedMismatchesN += T.nMM;
mappedInsN += T.nIns;
mappedDelN += T.nDel;
mappedInsL += T.lIns;
mappedDelL += T.lDel;
if (T.nExons==0)
return;
uint mappedL=0;
for (uint ii=0; ii<T.nExons; ii++) {
mappedL += T.exons[ii][EX_L];
};
for (uint ii=0; ii<T.nExons-1; ii++) {
if (T.canonSJ[ii]>=0) splicesN[T.canonSJ[ii]]++;
if (T.sjAnnot[ii]==1) splicesNsjdb++;
};
mappedBases += mappedL;
mappedPortion += double(mappedL)/double(Lread);
};
#define SETW1 setw(9)
#define SETW2 setw(8)
#define SETW3 setw(12)
void Stats::progressReportHeader(ofstream &progressStream) {
progressStream <<setw(15)<< "Time" <<SETW1<< "Speed" <<SETW3<< "Read" <<SETW1<< "Read" <<SETW1<< "Mapped" \
<<SETW1<< "Mapped" <<SETW1<< "Mapped" \
<<SETW1<< "Mapped" <<SETW1<< "Unmapped" <<SETW1<< "Unmapped" <<SETW1<< "Unmapped" <<SETW1<< "Unmapped"\
<< "\n";
progressStream <<setw(15)<< " " <<SETW1<< "M/hr" <<SETW3<< "number" <<SETW1<< "length" <<SETW1<< "unique" \
<<SETW1<< "length" <<SETW1<< "MMrate" \
<<SETW1<< "multi" <<SETW1<< "multi+" <<SETW1<< "MM" <<SETW1<< "short" <<SETW1<< "other"\
<< "\n"<<flush;
};
void Stats::progressReport(ofstream &progressStream) {
time_t timeCurrent;
time( &timeCurrent);
if (difftime(timeCurrent,timeLastReport)>=60.0 && readN>0) {//make the report
//progressStream.imbue(std::locale(""));
progressStream <<setw(15)<< timeMonthDayTime(timeCurrent) \
<<SETW1<< setiosflags(ios::fixed) << setprecision(1) \
<< double(readN)/1e6/difftime(timeCurrent,timeStartMap)*3600 \
<<SETW3<< readN \
<<SETW1<< (readN>0 ? readBases/readN : 0) \
<<SETW2<< (readN>0 ? double(mappedReadsU)/double(readN)*100 : 0) <<'%' \
<<SETW1<< (readN>0 ? double(mappedBases)/double(mappedReadsU) : 0)
<<SETW2<< (readN>0 ? double(mappedMismatchesN)/double(mappedBases)*100 : 0) <<'%' \
<<SETW2<< (readN>0 ? double(mappedReadsM)/double(readN)*100 : 0) <<'%'\
<<SETW2<< (readN>0 ? double(unmappedMulti)/double(readN)*100 : 0) <<'%'\
<<SETW2<< (readN>0 ? double(unmappedMismatch)/double(readN)*100 : 0) <<'%'\
<<SETW2<< (readN>0 ? double(unmappedShort)/double(readN)*100 : 0)<<'%'\
<<SETW2<< (readN>0 ? double(unmappedOther)/double(readN)*100 : 0) <<'%'\
<<"\n"<<flush;
timeLastReport=timeCurrent;
};
};
void Stats::reportFinal(ofstream &streamOut) {
int w1=50;
time( &timeFinish);
//<<setiosflags(ios::left)
streamOut <<setiosflags(ios::fixed) << setprecision(2) \
<<setw(w1)<< "Started job on |\t" << timeMonthDayTime(timeStart)<<"\n" \
<<setw(w1)<< "Started mapping on |\t" << timeMonthDayTime(timeStartMap)<<"\n" \
<<setw(w1)<< "Finished on |\t"<< timeMonthDayTime(timeFinish)<<"\n" \
<<setw(w1)<< "Mapping speed, Million of reads per hour |\t"<< double(readN)/1e6/difftime(timeFinish,timeStartMap)*3600<<"\n" \
<<"\n" \
<<setw(w1)<< "Number of input reads |\t" << readN <<"\n" \
<<setw(w1)<< "Average input read length |\t" << (readN>0 ? readBases/readN : 0) <<"\n" \
<<setw(w1)<< "UNIQUE READS:\n" \
<<setw(w1)<< "Uniquely mapped reads number |\t" << mappedReadsU <<"\n" \
<<setw(w1)<< "Uniquely mapped reads % |\t" << (readN>0 ? double(mappedReadsU)/double(readN)*100 : 0) <<'%'<<"\n" \
<<setw(w1)<< "Average mapped length |\t" << (mappedReadsU>0 ? double(mappedBases)/double(mappedReadsU) : 0) <<"\n";
streamOut <<setw(w1)<< "Number of splices: Total |\t" << splicesN[0]+splicesN[1]+splicesN[2]+splicesN[3]+splicesN[4]+splicesN[5]+splicesN[6]<< "\n" \
<<setw(w1)<< "Number of splices: Annotated (sjdb) |\t" << splicesNsjdb << "\n" \
<<setw(w1)<< "Number of splices: GT/AG |\t" << splicesN[1]+splicesN[2] << "\n" \
<<setw(w1)<< "Number of splices: GC/AG |\t" << splicesN[3]+splicesN[4] << "\n" \
<<setw(w1)<< "Number of splices: AT/AC |\t" << splicesN[5]+splicesN[6] << "\n" \
<<setw(w1)<< "Number of splices: Non-canonical |\t" << splicesN[0] << "\n";
streamOut <<setw(w1)<< "Mismatch rate per base, % |\t" << double(mappedMismatchesN)/double(mappedBases)*100 <<'%' <<"\n" \
<<setw(w1)<< "Deletion rate per base |\t" << (mappedBases>0 ? double(mappedDelL)/double(mappedBases)*100 : 0) <<'%' <<"\n" \
<<setw(w1)<< "Deletion average length |\t" << (mappedDelN>0 ? double(mappedDelL)/double(mappedDelN) : 0) <<"\n" \
<<setw(w1)<< "Insertion rate per base |\t" << (mappedBases>0 ? double(mappedInsL)/double(mappedBases)*100 : 0) <<'%' <<"\n" \
<<setw(w1)<< "Insertion average length |\t" << (mappedInsN>0 ? double(mappedInsL)/double(mappedInsN) : 0) <<"\n" \
<<setw(w1)<< "MULTI-MAPPING READS:\n" \
<<setw(w1)<< "Number of reads mapped to multiple loci |\t" << mappedReadsM <<"\n" \
<<setw(w1)<< "% of reads mapped to multiple loci |\t" << (readN>0 ? double(mappedReadsM)/double(readN)*100 : 0)<<'%' <<"\n" \
<<setw(w1)<< "Number of reads mapped to too many loci |\t" << unmappedMulti <<"\n" \
<<setw(w1)<< "% of reads mapped to too many loci |\t" << (readN>0 ? double(unmappedMulti)/double(readN)*100 : 0) <<'%' <<"\n" \
<<setw(w1)<< "UNMAPPED READS:\n" \
<<setw(w1)<< "Number of reads unmapped: too many mismatches |\t"<< unmappedMismatch<<"\n" \
<<setw(w1)<< "% of reads unmapped: too many mismatches |\t" << (readN>0 ? double(unmappedMismatch)/double(readN)*100 : 0) <<'%' <<"\n" \
<<setw(w1)<< "Number of reads unmapped: too short |\t" << unmappedShort <<"\n" \
<<setw(w1)<< "% of reads unmapped: too short |\t" << (readN>0 ? double(unmappedShort)/double(readN)*100 : 0) <<'%' <<"\n" \
<<setw(w1)<< "Number of reads unmapped: other |\t" << unmappedOther <<"\n" \
<<setw(w1)<< "% of reads unmapped: other |\t" << (readN>0 ? double(unmappedOther)/double(readN)*100 :0) <<'%'<<"\n" \
<<setw(w1)<< "CHIMERIC READS:\n" \
<<setw(w1)<< "Number of chimeric reads |\t" << chimericAll <<"\n" \
<<setw(w1)<< "% of chimeric reads |\t" << (readN>0 ? double(chimericAll)/double(readN)*100 :0) <<'%'<<"\n" <<flush;
};
void Stats::writeLines(ofstream &streamOut, const vector<int> outType, const string commStr, const string outStr) {
for (const auto& tt : outType) {
if (tt==1) {
if (outStr!="")
streamOut << commStr <<" "<< outStr <<"\n";
streamOut << commStr <<" "<< "Nreads " << readN <<"\t"<< "NreadsUnique " << mappedReadsU <<"\t"<< "NreadsMulti " << mappedReadsM << "\n";
};
};
};
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