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Jake Biesinger authored
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?
4cbfb094