Genomic intervals & annotation / Interval coverage
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For each interval in A four numbers are given: the number of overlapping B, the bases of A covered by B (overlapping B counted once), the length of A, and the fraction covered (bases ÷ length).
With genes as A and variants as B, the first number is the variant count per gene; with fixed windows as A and peaks as B, it shows how peaks are spread along the genome.
You can require the same or opposite strand, or a minimum overlap fraction, so only B with enough overlap are counted.
The fraction is printed with 7 decimals (single precision), as common command-line tools do; the “top 20” table helps to spot hotspots.
Output columns and number format match the default output of BEDTools coverage (Quinlan & Hall 2010, Bioinformatics 26:841), checked line by line on the same inputs.
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