Fully overlapping reads not detected (frequent in Amplicon data)
Hi @brentp,

I was checking the mosdepth _coverage_ procedure that looks at overlapping read pairs to avoid counting twice the coverage on the overlap section. I might be mistaken, but I think that the case were both reads are fully overlapping, as it frequently occurs with amplicon data, is not covered by the condition at this line (where it should be `rec.start <= rec.matepos`) : https://github.com/brentp/mosdepth/blob/a7622f289a2d19ef9270f1ab36c7410738580352/mosdepth.nim#L262

Best,
Jérôme.