Feature/makewindows with i ds1

Regression on -wao?

 even when there is no overlapping features in B.

an extra window was printed if the interval size evenly divided by the window size.

Allows user to name each window based on window number, source interval name, or both.

Add ignore options for features up- and downstream of A 

closestBed does some extra filtering of the hits returned by BedFile::allHits, but
it was previously assumed that each hit from allHits would be counted by closestBed.

This fix adds a check for the -t to make sure there are some hits in closestB and
updates numOverlaps when hits are filtered.

Maybe it would be better to add orientation-specific search to BedFile::allHits
instead of in closestBed?

 * requires -D and reuses its logic to determine orientation