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#include "Transcript.h"
Transcript::Transcript()
{
reset();
};
void Transcript::reset() {
extendL=0;
// for (uint ii=0;ii<4;ii++) {
// polyXlength[ii]=0;
// polyXnMM[ii]=0;
// };
primaryFlag=false;
rStart=0; roStart=0; rLength=0; gStart=0; gLength=0; //read and genomic coordinates
maxScore=0;
nMatch=0;
nMM=0;
nGap=0; lGap=0; lDel=0; lIns=0; nDel=0; nIns=0;
nUnique=nAnchor=0;
};
void Transcript::add(Transcript *trIn) {
maxScore+=trIn->maxScore;
nMatch+=trIn->nMatch;
nMM+=trIn->nMM;
nGap+=trIn->nGap; lGap+=trIn->lGap;
lDel+=trIn->lDel; nDel+=trIn->nDel;
lIns+=trIn->lIns; nIns+=trIn->nIns;
nUnique+=trIn->nUnique;
};
void Transcript::extractSpliceJunctions(vector<array<uint64,2>> &sjOut, bool &annotYes)
{
annotYes=true;
for (uint64 iex=0; iex<nExons-1; iex++) {//record all junctions
if (canonSJ[iex]>=0) {//only record junctions, not indels or mate gap
array<uint64,2> sj;
sj[0]=exons[iex][EX_G]+exons[iex][EX_L];//start
sj[1]=exons[iex+1][EX_G] - sj[0]; //gap
sjOut.push_back(sj);
if (sjAnnot[iex]==0)
annotYes=false;//if one of the SJs is unannoated, annotYes=false
};
};
};
uint64 Transcript::chrStartLengthExtended()
{
uint64 start1 = cStart - exons[0][EX_R];
uint64 length1 = exons[nExons-1][EX_G] + Lread - exons[nExons-1][EX_R] - exons[0][EX_G] + exons[0][EX_R];
return (start1 << 32) | length1;
};
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