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#include "SoloReadFeature.h"
#include "serviceFuns.cpp"
#include "SequenceFuns.h"
#include "ReadAnnotations.h"
#include "SoloReadBarcode.h"
class ReadSoloFeatures {
public:
uint32 gene;
vector<array<uint64,2>> sj;
bool sjAnnot;
uint32 indAnnotTr; //index of the annotated transcript
Transcript **alignOut;
};
uint32 outputReadCB(fstream *streamOut, const uint64 iRead, const int32 featureType, SoloReadBarcode &soloBar, const ReadSoloFeatures &reFe, const ReadAnnotations &readAnnot);
void SoloReadFeature::record(SoloReadBarcode &soloBar, uint nTr, Transcript **alignOut, uint64 iRead, ReadAnnotations &readAnnot)
{
if (pSolo.type==0 || soloBar.cbMatch<0)
return;
ReadSoloFeatures reFe;
reFe.alignOut=alignOut;
uint32 nFeat=0; //number of features in this read (could be >1 for SJs)
if (nTr==0) {//unmapped
stats.V[stats.nUnmapped]++;
} else {
switch (featureType) {
case SoloFeatureTypes::Gene :
case SoloFeatureTypes::GeneFull :
{
set<uint32> *readGe=( featureType==SoloFeatureTypes::Gene
? &readAnnot.geneConcordant : &readAnnot.geneFull ); //for Gene or GeneFull
if (readGe->size()==0) {//check genes
stats.V[stats.nNoFeature]++;//no gene
} else if (readGe->size()>1) {
stats.V[stats.nAmbigFeature]++;//multigene
if (nTr>1)
stats.V[stats.nAmbigFeatureMultimap]++;//multigene caused by multimapper
} else {//good gene
reFe.gene = *readGe->begin();
reFe.indAnnotTr = ( featureType==SoloFeatureTypes::Gene ? readAnnot.geneConcordantTr : readAnnot.geneFullTr );
nFeat = outputReadCB(streamReads, (readInfoYes ? iRead : (uint64)-1), featureType, soloBar, reFe, readAnnot);
};
};
break;
case SoloFeatureTypes::SJ :
if (nTr>1) {//reject all multimapping junctions
stats.V[stats.nAmbigFeatureMultimap]++;
} else if (readAnnot.geneConcordant.size()>1){//for SJs, still check genes, no feature if multi-gene
stats.V[stats.nAmbigFeature]++;
} else {//one gene or no gene
alignOut[0]->extractSpliceJunctions(reFe.sj, reFe.sjAnnot);
if ( reFe.sj.empty() || (reFe.sjAnnot && readAnnot.geneConcordant.size()==0) ) {//no junctions, or annotated junction but no gene (i.e. read does not fully match transcript)
stats.V[stats.nNoFeature]++;
} else {//good junction
reFe.indAnnotTr=0;
nFeat = outputReadCB(streamReads, (readInfoYes ? iRead : (uint64)-1), featureType, soloBar, reFe, readAnnot);
};
};
break;
case SoloFeatureTypes::Transcript3p :
if (readAnnot.transcriptConcordant.size()==0 || soloBar.cbMatch>1) {//do not record ambiguous CB
stats.V[stats.nNoFeature]++;
} else {
nFeat = outputReadCB(streamReads, iRead, featureType, soloBar, reFe, readAnnot);
};
if (readAnnot.transcriptConcordant.size()==1 && readAnnot.transcriptConcordant[0][1] < transcriptDistCount.size()) {
//read maps to one transcript - use for distTTS distribution function
transcriptDistCount[readAnnot.transcriptConcordant[0][1]]++;
};
break;
case SoloFeatureTypes::Velocyto :
//different record: iRead, nTr, tr1, type1, tr2, type2 ...
if (readAnnot.trVelocytoType.size()>0) {//otherwise, no gene
sort(readAnnot.trVelocytoType.begin(), readAnnot.trVelocytoType.end(),
[](const trTypeStruct &t1, const trTypeStruct &t2) {return t1.tr < t2.tr;});
*streamReads << iRead <<' '<< readAnnot.trVelocytoType.size();
for (auto &tt: readAnnot.trVelocytoType)
*streamReads <<' '<< tt.tr <<' '<< (uint32) tt.type;
*streamReads <<'\n';
nFeat=1;
} else {
stats.V[stats.nNoFeature]++;
};
break; //no need to go with downstream processing
};//switch (featureType)
};//if (nTr==0)
if (nFeat==0 && readInfoYes) {//no feature, but readInfo requested
outputReadCB(streamReads, iRead, (uint32)-1, soloBar, reFe, readAnnot);
};
if (nFeat==0)
return; //no need to record the number of reads per CB
if (pSolo.cbWLyes) {//WL
for (auto &cbi : soloBar.cbMatchInd)
cbReadCount[cbi] += nFeat;
} else {//no WL
cbReadCountMap[soloBar.cbMatchInd[0]] += nFeat;
};
return;
};
uint32 outputReadCB(fstream *streamOut, const uint64 iRead, const int32 featureType, SoloReadBarcode &soloBar, const ReadSoloFeatures &reFe, const ReadAnnotations &readAnnot)
{
/*format of the temp output file
* UMI [iRead] type feature* cbMatchString
* 0=exact match, 1=one non-exact match, 2=multipe non-exact matches
* gene or sj[0] sj[1]
* CB or nCB {CB Qual, ...}
*/
if (soloBar.pSolo.type==soloBar.pSolo.SoloTypes::SmartSeq && featureType!=-1) {//need to calculate "UMI" from align start/end
soloBar.umiB=reFe.alignOut[reFe.indAnnotTr]->chrStartLengthExtended();
};
uint64 nout=1;
switch (featureType) {
case -1 :
//no feature, output for readInfo
*streamOut << soloBar.umiB <<' '<< iRead <<' '<< -1 <<' '<< soloBar.cbMatch <<' '<< soloBar.cbMatchString <<'\n';
break;
case SoloFeatureTypes::Gene :
case SoloFeatureTypes::GeneFull :
//just gene id
*streamOut << soloBar.umiB <<' ';//UMI
if ( iRead != (uint64)-1 )
*streamOut << iRead <<' ';//iRead
*streamOut << reFe.gene <<' '<< soloBar.cbMatch <<' '<< soloBar.cbMatchString <<'\n';;
break;
case SoloFeatureTypes::SJ :
//sj - two numbers, multiple sjs per read
for (auto &sj : reFe.sj) {
*streamOut << soloBar.umiB <<' ';//UMI
if ( iRead != (uint64)-1 )
*streamOut << iRead <<' ';//iRead
*streamOut << sj[0] <<' '<< sj[1] <<' '<< soloBar.cbMatch <<' '<< soloBar.cbMatchString <<'\n';
};
nout=reFe.sj.size();
break;
case SoloFeatureTypes::Transcript3p :
//transcript,distToTTS structure
*streamOut << soloBar.cbMatchString <<' ';
*streamOut << soloBar.umiB <<' ';
*streamOut << readAnnot.transcriptConcordant.size();
for (auto &tt: readAnnot.transcriptConcordant) {
*streamOut <<' '<< tt[0] <<' '<< tt[1];
};
if ( iRead != (uint64)-1 )
*streamOut <<' '<< iRead;//iRead
*streamOut <<'\n';
nout=1;
break;
}; //switch (featureType)
return nout;
};
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