Adding --maxVariantFrac and --minOppositeDepth to MethylDackel (Bwameth option)

[LucaZanella15]

Description of feature

Hi all,

I think that adding the possibility to provide the --maxVariantFrac option (and its --minOppositeDepth counterpart, by default set to 0) would be of great value.

The possibility to switch on and off --keepDupes (currently by default properly being on) would also be useful to account for current EM-seq library preparation technologies that produce complex libraries that have low probability of fragments having the same start and stop positions unless they are true duplicates

[sateeshperi]

hi @LucaZanella15 couldn't these set in ext.args of methydackel ? could you explain more on why it would be good to add by default ?