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#include "Solo.h"
#include "TimeFunctions.h"
#include "streamFuns.h"
Solo::Solo(ReadAlignChunk **RAchunkIn, Parameters &Pin, Transcriptome &inTrans)
: RAchunk(RAchunkIn), P(Pin), Trans(inTrans), pSolo(P.pSolo)
{
if ( pSolo.type == 0 )
return;
readBarSum = new SoloReadBarcode(P);
if ( pSolo.type == pSolo.SoloTypes::CB_samTagOut )
return;
soloFeat = new SoloFeature*[pSolo.nFeatures];
for (uint32 ii=0; ii<pSolo.nFeatures; ii++)
soloFeat[ii] = new SoloFeature(P, RAchunk, Trans, pSolo.features[ii], readBarSum, soloFeat);
};
///////////////////////////////////////////////////////////////////////////////////// post-mapping processing only
//overloaded: only soloCellFiltering
Solo::Solo(Parameters &Pin, Transcriptome &inTrans)
: P(Pin), Trans(inTrans), pSolo(P.pSolo)
{
if ( P.runMode != "soloCellFiltering" )
return; //passing through, return back to executing STAR
time_t timeCurrent;
time( &timeCurrent);
*P.inOut->logStdOut << timeMonthDayTime(timeCurrent) << " ..... starting SoloCellFiltering" <<endl;
soloFeat = new SoloFeature*[1];
soloFeat[0] = new SoloFeature(P, NULL, Trans, -1, NULL, soloFeat);
soloFeat[0]->loadRawMatrix();
soloFeat[0]->cellFiltering();
time( &timeCurrent);
*P.inOut->logStdOut << timeMonthDayTime(timeCurrent) << " ..... finished successfully\n" <<flush;
P.inOut->logMain << "ALL DONE!\n" << flush;
exit(0);
};
////////////////////////////////////////////////////////////////////////////////////
void Solo::processAndOutput()
{
if (pSolo.type==0 )
return;
{//collect barcode statistics
if (pSolo.cbWLyes) {//now we can define WL and counts
for (int ii=0; ii<P.runThreadN; ii++) {
readBarSum->addCounts(*RAchunk[ii]->RA->soloRead->readBar);
readBarSum->addStats(*RAchunk[ii]->RA->soloRead->readBar);
delete RAchunk[ii]->RA->soloRead->readBar; //not needed anymore
};
};
ofstream *statsStream = &ofstrOpen(P.outFileNamePrefix+pSolo.outFileNames[0]+"Barcodes.stats",ERROR_OUT, P);
readBarSum->statsOut(*statsStream);
statsStream->close();
//pseudocounts
if (pSolo.CBmatchWL.mm1_multi_pc) {
for (uint32 ii=0; ii<pSolo.cbWLsize; ii++) {
readBarSum->cbReadCountExact[ii]++;//add one to exact counts
};
};
};
if (pSolo.type==pSolo.SoloTypes::CB_samTagOut)
return;
{//process all features
*P.inOut->logStdOut << timeMonthDayTime() << " ..... started Solo counting\n" <<flush;
P.inOut->logMain << timeMonthDayTime() << " ..... started Solo counting\n" <<flush;
for (uint32 ii=0; ii<pSolo.nFeatures; ii++) {
soloFeat[ii]->processRecords();
//if (!pSolo.readInfoYes[soloFeat[ii]->featureType]) {
// delete soloFeat[ii];
//};
};
*P.inOut->logStdOut << timeMonthDayTime() << " ..... finished Solo counting\n" <<flush;
P.inOut->logMain << timeMonthDayTime() << " ..... finished Solo counting\n" <<flush;
};
};
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