Minor changes before re-implementing Solo temp files.
@@ -44,39 +44,39 @@ void SoloReadFeature::record(SoloReadBarcode &soloBar, uint nTr, set<uint32> &re
readGe = &readGeneFull;
};
- bool featYes=true;
+ bool readFeatYes=true;
if (featureType==0 || featureType==2) {//genes
//check genes, return if no gene of multimapping
if (readGe->size()==0) {
stats.V[stats.nNoFeature]++;
- featYes=false;
+ readFeatYes=false;
};
if (readGe->size()>1) {
stats.V[stats.nAmbigFeature]++;
if (nTr>1)
stats.V[stats.nAmbigFeatureMultimap]++;
- featYes=false;
+ readFeatYes=false;
};
} else if (featureType==1) {//SJs
if (nTr>1) {//reject all multimapping junctions
stats.V[stats.nAmbigFeatureMultimap]++;
- featYes=false;
+ readFeatYes=false;
} else {//for SJs, still check genes, return if multi-gene
if (readGene.size()>1) {
stats.V[stats.nAmbigFeature]++;
- featYes=false;
+ readFeatYes=false;
} else {//one gene or no gene
bool sjAnnot;
alignOut->extractSpliceJunctions(readSJs, sjAnnot);
if ( readSJs.empty() || (sjAnnot && readGene.size()==0) ) {//no junctions, or annotated junction but no gene (i.e. read does not fully match transcript)
stats.V[stats.nNoFeature]++;
- featYes=false;
+ readFeatYes=false;
};
};
};
};
- if (!featYes)
+ if (!readFeatYes)
return;
if (!readInfoYes)
