#ifndef OUT_SJ_DEF

#define OUT_SJ_DEF

#include "Parameters.h"

class Junction {//one junction

public:

const static uint startP=0;

const static uint gapP=startP+sizeof(uint);

const static uint strandP=gapP+sizeof(uint32);

const static uint motifP=strandP+sizeof(char);

const static uint annotP=motifP+sizeof(char);

const static uint countUniqueP=annotP+sizeof(char);

const static uint countMultipleP=countUniqueP+sizeof(uint32);

const static uint overhangLeftP=countMultipleP+sizeof(uint32);

const static uint overhangRightP=overhangLeftP+sizeof(uint16);

uint *start;

uint32 *gap;

char *strand, *motif, *annot;

uint32 *countUnique, *countMultiple;

uint16 *overhangLeft, *overhangRight;

const static uint dataSize=overhangRightP+sizeof(uint16);

void junctionPointer(char* sjPoint, uint isj);

void outputStream(ostream &outStream, Parameters* P);

void collapseOneSJ(char* isj1P, char* isjP, Parameters* P);

};

class OutSJ {

public:

//all junctions

char* data; //sj array[Njunctions][dataSize]

uint N; //number of junctions stored

Junction oneSJ;

Parameters *P;

OutSJ(uint nSJmax, Parameters *P);

void collapseSJ();//collapse the junctions in data

// int compareSJ(void* i1, void* i2);

};

int compareSJ(const void* i1, const void* i2); //external functions

#endif