Changed pre-filtering of short overhangs - only done for chimerically split mates. Result are slightly different from the previous commit.
@@ -27,7 +27,8 @@ bool ChimericAlign::chimericCheck()
//TTGAGGTGAAGTTCAAAGATGTGGCTGGCTGTGAGGAGGCCGAGCTAGAGATCATGGAATTTGTGAATTTCTTGAA
//} else
- chimGood = chimGood && al1->exons[ex1][EX_L] >= pCh.junctionOverhangMin && al2->exons[ex2][EX_L] >= pCh.junctionOverhangMin;//junction overhangs too short
+ //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;
};
