String qualHead2 = qual2.substring(0, overlap); MutableFloat mismatchFrac = new MutableFloat(0);
MutableFloat bestTestLoglik = new MutableFloat(-9999999);
String qualHead2 = qual2.substring(0, overlap); MutableFloat mismatchFrac = new MutableFloat(0);
MutableFloat bestTestLoglik = new MutableFloat(-9999999);