KamilSJaron
Previnting smudgeplot annotations with L / U too close to each other
Some people run into troubles (#55) for picking L and U too close to each other and then non-having any kmers with low minor allele coverage ratio. I don't necessarily think it's too wrong to refuse to annotate such smudgeplots, but perhaps we should implement something that either stops smudgeplot from running further, or simply refuse to annotate.
This sort of relates to my long-standing desire to allow smudgeplot to run without any guess of the ploidy (simply plot the structure) perhaps if I would separate better the plotting and the annotation part it would be also easy to allow plotting without annotation if there will be any trouble in the annotation procedure (as the one described above).
New version of smudgeplot (https://github.com/KamilSJaron/smudgeplot/releases/tag/v0.2.5) won't drop the error HOWEVER it might still be a good idea to add the warning or even hard-block to make user chose L and U more wisely.
Sidenote: updating the cutoff algorithm would help a lot with this too, because majority of users simply run is as "the silver bullet" without challenging sanity of those values (i.e. trusting my naive algorithm more than their of judgement which they shouldn't obviously :-) ).