byte[]miniReference = null;
if(reference != null) {
miniReference = Arrays.copyOfRange(reference, (int) (windowStart - 1), (int) (windowEnd - 1));
}
BamGenomeWindow w = detailed ? new BamDetailedGenomeWindow(name,windowStart,windowEnd,miniReference) :
new BamGenomeWindow(name,windowStart,windowEnd,miniReference);
if (selectedRegionsAvailable) {
calculateRegionsLookUpTableForWindow(w);
}