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#include "ChimericAlign.h"
ChimericAlign::ChimericAlign(ChimericSegment &seg1in, ChimericSegment &seg2in, int chimScoreIn, Genome &genomeIn, ReadAlign *RAin)
: seg1(seg1in), seg2(seg2in),chimScore(chimScoreIn), RA(RAin), P(seg1in.P), pCh(P.pCh), mapGen(genomeIn) {
stitchingDone=false;
al1=&seg1.align;
al2=&seg2.align;
if (al1->roStart > al2->roStart)
swap (al1,al2);
ex1 = al1->Str==1 ? 0 : al1->nExons-1;
ex2 = al2->Str==0 ? 0 : al2->nExons-1;
};
bool ChimericAlign::chimericCheck() {
bool chimGood=true;
chimGood = chimGood && al1->exons[ex1][EX_iFrag] <= al2->exons[ex2][EX_iFrag];//otherwise - strange configuration, both segments contain two mates
//if ( trChim[0].exons[e0][EX_iFrag] > trChim[1].exons[e1][EX_iFrag] ) {//strange configuration, rare, similar to the next one
// chimN=0;//reject such chimeras
//good test example:
//CTTAGCTAGCAGCGTCTTCCCAGTGCCTGGAGGGCCAGTGAGAATGGCACCCTCTGGGATTTTTGCTCCTAGGTCT
//TTGAGGTGAAGTTCAAAGATGTGGCTGGCTGTGAGGAGGCCGAGCTAGAGATCATGGAATTTGTGAATTTCTTGAA
//} else
//junction overhangs too short for chimerically spliced mates
chimGood = chimGood && (al1->exons[ex1][EX_iFrag] < al2->exons[ex2][EX_iFrag] || (al1->exons[ex1][EX_L] >= pCh.junctionOverhangMin && al2->exons[ex2][EX_L] >= pCh.junctionOverhangMin) );
return chimGood;
};
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