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/*
* Created by Fahimeh Mirhaj on 6/10/19.
*/
using namespace std;
#include "SpliceGraph.h"
#include "GTF.h"
SpliceGraph::SpliceGraph (SuperTranscriptome &superTrome, Parameters &P, ReadAlign *RA) : superTrome(superTrome), P(P), RA(RA)
{
//find candidate superTr
superTrSeedCount = new typeSuperTrSeedCount[2*superTrome.N];//TODO: for stranded data, do not need 2nd strand
//Smith-Waterman
scoringMatrix = new typeAlignScore*[superTrome.sjDonorNmax+2];
scoreTwoColumns[0] = new typeAlignScore[maxSeqLength];
scoreTwoColumns[1] = new typeAlignScore[maxSeqLength];
for(uint32 ii = 0; ii < superTrome.sjDonorNmax+2; ii++) {
scoringMatrix[ii] = new typeAlignScore[maxSeqLength];//TODO make it a user parameter
};
sjDindex = new uint32[superTrome.sjDonorNmax];
//rowCol.reserve(100000);
//rowSJ.reserve(100000);
//blockCoord.reserve(100000);
//blockSJ.reserve(10000);
};
SpliceGraph::~SpliceGraph() {
for(uint i = 0; i < maxSeqLength; i++) {
delete[] scoringMatrix[i];
};
delete[] scoringMatrix;
};
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