I'm learning Bioconductor but can't seem to understand how Biostrings::coverage() works.
During the class I was taught that coverage "counts, for each integer, how many ranges overlap the integer.".
Another definition I found in the documentation of the IRanges package (coverage methods) is "For each position in the space underlying a set of ranges, counts the number of ranges that cover it."
So if I have the following IRanges
> ir <- IRanges(start = c(2,6), width = 2)
and compute the coverage
I would expect to get back an Rle where as Values I have all the integer that a covered by the IRanges (meaning 2 3 6 7) and as Lengths I have the number of times those integer are "covered" by the ranges in the IRanges. In this example this would mean
integer-Rle of length 4 with 4 runs Lengths: 1 1 1 1 Values : 2 3 6 7
Except that the returned Rle is something entirely different:
> coverage(ir) integer-Rle of length 7 with 4 runs Lengths: 1 2 2 2 Values : 0 1 0 1
 0 1 1 0 0 1 1
Can someone explain me why are there 0s an 1s as Values when neither of this two integer is actually part of the input IRanges? And why do they repeat? I simply can't understand how this Rle is representing the inputted IRanges...