Handling homozygous genomes with Arched version

[LeoVincenzi]

Dear developers,
I'm contacting you with a question about the new version of Smudgeplot just released.
Comparing it with the old versions, I've noticed that the command

smudgeplot.py plot

do not include the option --homozygous to handle highly homozygous genomes anymore.
I was then wondering why and if there is a new way to handle those cases with the last updates.
Thank you!
Leo

[KamilSJaron]

That is a good point. We should add that flag back.

We tried to make it modular to the extend you could make these plots with any coverage you think is right, so you could make those assessments yourself, but none of that is very well documented at the moment. The tool is must better in creating intuitively interpretable plots now, which I hope overweight this temporal mess in lacking functionalities and poor documentation.