Retention scores systematically underestimated

[kbseah]

Both MILRET and MILRAA count only reads that completely span an IES and either contain an insert or do not. If inserts/IESs are too long, the mapping will have a clip instead of an insert. For short IESs this is negligible, but as IESs are longer, a greater proportion of mapped IES+ reads will have clips, but these are currently ignored in calculating the retention score.