int nMera = 0;
string chimeraRefSeq = "";
- if(bestSequenceMismatch - minMismatchToChimera <= 3){
- nMera = 1;
- chimeraRefSeq = referenceSeqs[bestMatch];
- }
- else {
-
+ if(bestSequenceMismatch - minMismatchToChimera > 3 || (minMismatchToChimera == 0 && bestSequenceMismatch != 0)){
+
nMera = 2;
chimeraRefSeq = stitchBimera(leftParentBi, rightParentBi, breakPointBi);
// }
}
+ else{
+ nMera = 1;
+ chimeraRefSeq = referenceSeqs[bestMatch];
+ }
+
+
double distToChimera = calcDistToChimera(querySeq, chimeraRefSeq);
// double loonIndex = calcLoonIndex(querySeq, referenceSeqs[leftParentBi], referenceSeqs[rightParentBi], breakPointBi, binMatrix);