When counting the number of available sites in PairwiseDifferencesWindow, the current algorithm use interval.size() - counter.countNsRegion(interval) - 1 to maintain compatibility regarding previous (and not tested) implementations.
Thus, we should invertigate if this behaviour is what we expect. The available sites should be the same as the bases included in the window if the number of Ns within the window is 0. This is related with #23 because we will require to change this if it is not working.
When counting the number of available sites in
PairwiseDifferencesWindow, the current algorithm useinterval.size() - counter.countNsRegion(interval) - 1to maintain compatibility regarding previous (and not tested) implementations.Thus, we should invertigate if this behaviour is what we expect. The available sites should be the same as the bases included in the window if the number of Ns within the window is 0. This is related with #23 because we will require to change this if it is not working.