double distToChimera = calcDistToChimera(querySeq, chimeraRefSeq);
// double loonIndex = calcLoonIndex(querySeq, referenceSeqs[leftParentBi], referenceSeqs[rightParentBi], breakPointBi, binMatrix);
double distToChimera = calcDistToChimera(querySeq, chimeraRefSeq);
// double loonIndex = calcLoonIndex(querySeq, referenceSeqs[leftParentBi], referenceSeqs[rightParentBi], breakPointBi, binMatrix);