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#ifndef H_ReadAnnotations
#define H_ReadAnnotations
#include "IncludeDefine.h"
#include "SoloCommon.h"
#include "SoloFeatureTypes.h"
class ReadAnnotFeature {//annotations for one feature
public:
set<uint32> fSet; //set of genes for this read
vector<set<uint32>> fAlign; //gene for each alignment of this read
uint32 ovType;
enum overlapTypes {none, exonic, exonicAS, exonic50p, exonic50pAS, intronic, intronicAS, intergenic, N};
void reset() {
fSet={}; fAlign={}; ovType = 0;
};
};
class ReadAnnotations {
public:
//set<uint32> geneFull, geneFull_Ex50pAS, geneFull_ExonOverIntron, geneConcordant;
//uint32 geneFullTr, geneFull_Ex50pAS_Tr, geneFull_ExonOverIntron_Tr, geneConcordantTr; //index of the annotated align - for multimappers that aligned to one gene only
//vector<int32> geneFull_Al, geneFull_Ex50pAS_Al, geneFull_ExonOverIntron_Al, geneConcordant_Al; //gene for each align
array<ReadAnnotFeature, SoloFeatureTypes::N> annotFeatures;
vector<array<uint32,2>> transcriptConcordant;
vector<int32> geneExonOverlap;
array<uint32,2> geneVelocytoSimple;//first element is gene, then counts of transcript types
vector<trTypeStruct> trVelocytoType;//first element is gene, then counts of transcript types
//vector<array<uint64,2>> sj;
//bool sjAnnot;
void reset () {
transcriptConcordant = {};
trVelocytoType = {};
for (auto &raf : annotFeatures)
raf.reset();
};
};
#endif
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