Genomic intervals & annotation / Closest feature
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For each interval in A the nearest B is reported: distance 0 when they overlap; otherwise the gap in bases plus one (1 for book-ended intervals). When A’s chromosome has no B, the B columns are “.” and the distance is −1.
A common use is “nearest gene to each peak”: choose “relative to B’s strand” so negative values mean the peak lies upstream of the gene and positive values downstream; features without a strand follow reference coordinates.
“Ignore overlapping B” finds the nearest non-overlapping neighbour (for example the next gene); the direction limit is available with “relative to A’s strand” or “reference coordinates”.
Ties (equal distances on both sides, or several overlapping B) are all reported by default, so there may be more rows than intervals in A; choose “report the first” for one row each.
The histogram shows distances within the chosen range, to see whether intervals concentrate near features.
Binary search for the nearest neighbours on each side; distance definition, signs and tie rules match BEDTools closest (-d / -D ref|a|b, -io, -t) (Quinlan & Hall 2010, Bioinformatics 26:841), checked line by line on the same inputs.
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