Add command line switches for compact genomes

[lucventurini]

Mikado with its default configuration tends to discard small-ish genes that are within introns or nearby the UTR of other genes.

Moreover, its overlap checks can gather together genes that should be considered separate.

This behaviour is desirable in plant and mammalian genomes (where genes are relatively spaced apart) but, as noted by @francicco on his data, this is not desirable for organisms that have compact genomes and where genes tend to overlap.

Having command line switches that set multiple values to sane defaults for compact genomes with lots of nested or overlapping genes would be desirable.

[francicco]

Hi, any update about that?
Cheers
F