Minor comment improvements.
Store 3' end strand for region (as well, as before and now superfluously, for each 3' end) when getting 3' ends.
Store 3' end strand for region (as well, as before and now superfluously, for each 3' end) when merging 3' ends.
Store 3' end strand for region (as well, as before and now superfluously, for each 3' end) when filtering 3' ends.
Use 3' end strand for region when choosing 3' end, if no 3' end.
Tidy.
New release.