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#ifndef CODE_Transcript
#define CODE_Transcript
#include "IncludeDefine.h"
#include "Parameters.h"
#include "Variation.h"
#include "Genome.h"
#include <set>
class Transcript {
public:
uint exons[MAX_N_EXONS][EX_SIZE]; //coordinates of all exons: r-start, g-start, length
vector <array<uint32,2>> cigar; //new way to record alignments, with CIGAR operations. For now, only used by splice-graph
uint shiftSJ[MAX_N_EXONS][2]; //shift of the SJ coordinates due to genomic micro-repeats
int canonSJ[MAX_N_EXONS]; //canonicity of each junction
uint8 sjAnnot[MAX_N_EXONS]; //anotated or not
uint8 sjStr[MAX_N_EXONS]; //strand of the junction
uint intronMotifs[3];
uint8 sjMotifStrand;
bool sjYes;
uint nExons; //number of exons in the read transcript
//variables from ReadAlign
uint *readLengthOriginal, *readLength;
uint Lread, readLengthPairOriginal;
uint iRead; //read identifier
uint readNmates;
char *readName;
int iFrag; //frag number of the transcript, if the the transcript contains only one frag
//loci
uint rStart, roStart, rLength, gStart, gLength, cStart; //read, original read, and genomic start/length, chromosome start
uint Chr,Str,roStr; //chromosome and strand and original read Strand
uint32 haploType; //haplotype index for diploid genome
bool primaryFlag;
uint nMatch;//min number of matches
uint nMM;//max number of mismatches
uint mappedLength; //total mapped length, sum of lengths of all blocks(exons)
uint extendL; //extension length
intScore maxScore; //maximum Score
uint nGap, lGap; //number of genomic gaps (>alignIntronMin) and their total length
uint nDel; //number of genomic deletions (ie genomic gaps)
uint nIns; //number of (ie read gaps)
uint lDel; //total genomic deletion length
uint lIns; //total genomic insertion length
uint nUnique, nAnchor; //number of unique pieces in the alignment, number of anchor pieces in the alignment
vector <int32> varInd;
vector <int32> varGenCoord, varReadCoord ;
vector <char> varAllele;
//annotations
std::set <uint32> alignGenes;
Transcript(); //resets to 0
void reset(); //reset to 0
void resetMapG(); // reset map to 0
void resetMapG(uint); // reset map to 0 for Lread bases
void add(Transcript*); // add
intScore alignScore(char **Read1, char *G, Parameters &P);
int variationAdjust(const Genome &mapGen, char *R);
string generateCigarP(); //generates CIGAR
void peOverlapSEtoPE(uint* mSta, const Transcript &t);
void extractSpliceJunctions(vector<array<uint64,2>> &sjOut, bool &annotYes);
uint64 chrStartLengthExtended();
bool transformGenome(Genome &genOut, Transcript & A);
bool convertGenomeCigar(Genome &genOut, Transcript & A);
private:
};
#endif
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