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#include "SoloFeature.h"
#include "streamFuns.h"
#include "TimeFunctions.h"
#include "SequenceFuns.h"
#include "Stats.h"
#include "GlobalVariables.h"
void SoloFeature::sumThreads()
{
//stats
nReadsInput=g_statsAll.readN+1; //reserve 1 extra
///////////////////////////// collect RAchunk->RA->soloRead->readFeat
for (int ii=0; ii<P.runThreadN; ii++) {//point to
readFeatAll[ii]= RAchunk[ii]->RA->soloRead->readFeat[pSolo.featureInd[featureType]];
readFeatAll[ii]->streamReads->flush();
readFeatSum->addCounts(*readFeatAll[ii]);
};
// if WL was not defined
if (!pSolo.cbWLyes) {//now we can define WL and counts ??? we do not need to do it for every feature???
pSolo.cbWLsize=readFeatSum->cbReadCountMap.size();
pSolo.cbWL.resize(pSolo.cbWLsize);
pSolo.cbWLstr.resize(pSolo.cbWLsize);
readFeatSum->cbReadCount.resize(pSolo.cbWLsize);
readBarSum->cbReadCountExact.resize(pSolo.cbWLsize);
if (pSolo.CBtype.type==1) {//sequence cb
uint64 icb=0;
for (auto &cb : readFeatSum->cbReadCountMap) {
pSolo.cbWL[icb] = cb.first;
pSolo.cbWLstr[icb] = convertNuclInt64toString(pSolo.cbWL[icb],pSolo.cbL);
readFeatSum->cbReadCount[icb]=cb.second;
readBarSum->cbReadCountExact[icb]=cb.second;
icb++;
};
} else if (pSolo.CBtype.type==2) {//string cb
vector< std::unordered_map<string,uint32>::iterator > cbiter(pSolo.CBtype.strMap.size());
for (auto cbi=pSolo.CBtype.strMap.begin(); cbi!=pSolo.CBtype.strMap.end(); cbi++)
cbiter[cbi->second] = cbi;
uint64 icb=0;
for (auto &cb : readFeatSum->cbReadCountMap) {
pSolo.cbWL[icb] = cb.first;
pSolo.cbWLstr[icb] = cbiter[cb.first]->first;
readFeatSum->cbReadCount[icb]=cb.second;
readBarSum->cbReadCountExact[icb]=cb.second;
icb++;
};
};
//pseudocounts
if (pSolo.CBmatchWL.mm1_multi_pc) {
for (uint32 ii=0; ii<pSolo.cbWLsize; ii++) {
readBarSum->cbReadCountExact[ii]++;//add one to exact counts
};
};
};
// if restarting from _STARtmp/solo* file
if (P.runRestart.type==1) {//this could happen if the run is restarted. Would be better to save/load cbReadCount, or recalculate it from
for (int ii=0; ii<P.runThreadN; ii++) {
readFeatAll[ii]->streamReads->clear(); //just in case EOF was reached in previous reading
readFeatAll[ii]->streamReads->seekg(0,ios::beg);
string line1;
while (std::getline(*readFeatAll[ii]->streamReads, line1)) {
istringstream line1stream(line1);
uint64 cb1;
line1stream >> cb1 >> cb1 >> cb1;
if (featureType==SoloFeatureTypes::SJ)
line1stream >> cb1;
line1stream >> cb1;
//if (cb1>readFeatSum->cbReadCount.size())
// continue;//this should not happen!
readFeatSum->cbReadCount[cb1]++;
};
};
};
//detected CBs
nCB=0;nReadsMapped=0;
for (uint32 ii=0; ii<pSolo.cbWLsize; ii++) {
if (readFeatSum->cbReadCount[ii]>0) {
nCB++;
nReadsMapped += readFeatSum->cbReadCount[ii];
};
};
indCBwl.resize(pSolo.cbWLsize, (uint32) -1);
indCB.resize(nCB);
nCB=0;//will count it again below
for (uint32 ii=0; ii<pSolo.cbWLsize; ii++) {
if (readFeatSum->cbReadCount[ii]>0) {
indCB[nCB]=ii;
indCBwl[ii]=nCB;
++nCB;
};
};
};
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