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#ifndef H_Genome
#define H_Genome
#include "IncludeDefine.h"
#include "Parameters.h"
#include "PackedArray.h"
#include "SharedMemory.h"
#include "Variation.h"
#include "SuperTranscriptome.h"
class GTF;
class Genome {
private:
key_t shmKey;
char *shmStart;
uint OpenStream(string name, ifstream & stream, uint size);
void HandleSharedMemoryException(const SharedMemoryException & exc, uint64 shmSize);
public:
Parameters &P;
ParametersGenome &pGe;
SharedMemory *sharedMemory;
enum {exT,exS,exE,exG,exL}; //indexes in the exonLoci array from GTF
char *G, *G1;
uint64 nGenome, nG1alloc;
PackedArray SA,SAinsert,SApass1,SApass2;
PackedArray SAi;
Variation *Var;
uint nGenomeInsert, nGenomePass1, nGenomePass2, nSAinsert, nSApass1, nSApass2;
//chr parameters
vector <uint64> chrStart, chrLength, chrLengthAll;
uint genomeChrBinNbases, chrBinN, *chrBin;
vector <string> chrName, chrNameAll;
map <string,uint64> chrNameIndex;
uint *genomeSAindexStart;//starts of the L-mer indices in the SAindex, 1<=L<=pGe.gSAindexNbases
uint nSA, nSAbyte, nChrReal;//genome length, SA length, # of chromosomes, vector of chromosome start loci
uint nGenome2, nSA2, nSAbyte2, nChrReal2; //same for the 2nd pass
uint nSAi; //size of the SAindex
unsigned char GstrandBit, SAiMarkNbit, SAiMarkAbsentBit; //SA index bit for strand information
uint GstrandMask, SAiMarkAbsentMask, SAiMarkAbsentMaskC, SAiMarkNmask, SAiMarkNmaskC;//maske to remove strand bit from SA index, to remove mark from SAi index
//SJ database parameters
uint sjdbOverhang, sjdbLength; //length of the donor/acceptor, length of the sj "chromosome" =2*pGe.sjdbOverhang+1 including spacer
uint sjChrStart,sjdbN; //first sj-db chr
uint sjGstart; //start of the sj-db genome sequence
uint *sjDstart,*sjAstart,*sjStr, *sjdbStart, *sjdbEnd; //sjdb loci
uint8 *sjdbMotif; //motifs of annotated junctions
uint8 *sjdbShiftLeft, *sjdbShiftRight; //shifts of junctions
uint8 *sjdbStrand; //junctions strand, not used yet
//sequence insert parameters
uint genomeInsertL; //total length of the sequence to be inserted on the fly
uint genomeInsertChrIndFirst; //index of the first inserted chromosome
//SuperTranscriptome genome
SuperTranscriptome *superTr;
Genome (Parameters &P, ParametersGenome &pGe);
//~Genome();
void freeMemory();
void genomeLoad();
void genomeOutLoad();
void chrBinFill();
void chrInfoLoad();
void genomeSequenceAllocate(uint64 nGenomeIn, uint64 &nG1allocOut, char*& Gout, char*& G1out);
void loadSJDB(string &genDir);
void insertSequences();
//void consensusSequence(); DEPRECATED
void genomeGenerate();
void writeChrInfo(const string dirOut);
void concatenateChromosomes(const vector<vector<uint8>> &vecSeq, const vector<string> &vecName, const uint64 padBin);
void writeGenomeSequence(const string dirOut);
//transform genome coordinates
struct {
bool convYes;
bool gapsAreJunctions;
Genome *g;
string convFile;
vector<array<uint64,3>> convBlocks;
uint64 nMinusStrandOffset;//offset for the (-) strand, typically=nGenomeReal
} genomeOut;
typedef struct {
uint64 pos;
int32 len;//0: SNV, <0: deletion; >0: insertion
array<string,2> seq;//sequence for SNV and insertions, empty for deletions
} VariantInfo;
void transformGenome(GTF *gtf) ;
void transformChrLenStart(map<string,vector<VariantInfo>> &vcfVariants, vector<uint64> &chrStart1, vector<uint64> &chrLength1);
void transformGandBlocks(map<string,vector<VariantInfo>> &vcfVariants, vector<uint64> &chrStart1, vector<uint64> &chrLength1, vector<array<uint64,3>> &transformBlocks, char *Gnew);
void transformBlocksWrite(vector<array<uint64,3>> &transformBlocks);
void transformExonLoci(vector<array<uint64,exL>> &exonLoci, vector<array<uint64,3>> &transformBlocks);
};
#endif
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