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#ifndef CODE_Transcriptome
#define CODE_Transcriptome
#include <set>
#include "IncludeDefine.h"
#include "Parameters.h"
#include "Transcript.h"
#include "Quantifications.h"
#include "AlignVsTranscript.h"
#include "ReadAnnotations.h"
class Transcriptome {
public:
string trInfoDir;
vector <string> trID, geID, geName, geBiotype; //transcript/gene IDs
uint32 nTr, nGe; //number of transcript/genes
uint *trS, *trE, *trEmax; //transcripts start,end,end-max
uint32 nEx; //number of exons
uint16 *trExN; //number of exons per transcript
uint32 *trExI; //index of the first exon for each transcript in exSE
uint8 *trStr; //transcript strand
uint32 *exSE; //exons start/end
uint32 *exLenCum; //cumulative length of previous exons
uint32 *trGene; //transcript to gene correspondence
uint32 *trLen; //transcript lengths
struct {//exon-gene structure for GeneCounts
uint64 nEx;//number of exons/genes
uint64 *s,*e, *eMax; //exon start/end
uint8 *str; //strand
uint32 *g, *t; //gene/transcript IDs
} exG;
struct {//geneFull structure
uint64 *s, *e, *eMax;
uint8 *str;
uint32 *g;
} geneFull;
Quantifications *quants;
//methods:
Transcriptome (Parameters &Pin); //create transcriptome structure, load and initialize parameters
uint32 quantAlign (Transcript &aG, Transcript *aTall);//transform coordinates for all aligns from genomic in RA to transcriptomic in RAtr
void geneCountsAddAlign(uint nA, Transcript **aAll, vector<int32> &gene1); //add one alignment to gene counts
void quantsAllocate(); //allocate quants structure
void quantsOutput(); //output quantification files
void geneFullAlignOverlap(uint nA, Transcript **aAll, int32 strandType, ReadAnnotations &readAnnot);
void classifyAlign (Transcript **alignG, uint64 nAlignG, ReadAnnotations &readAnnot);
private:
Parameters &P; //normal "genomic" parameters
};
#endif
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