Setting dentist parameters

When setting the parameters below, do these need to be included in the dentist.json config file? and if so in which section?

--max-insertion-error
--min-anchor-length
--min-reads-per-pile-up
--min-spanning-reads
--allow-single-reads
--join-policy

Look at the dentist.json config file structure in the repository to understand existing sections. Check command-line parsing code to see how parameters like --max-insertion-error are handled. Determine if these parameters belong in the config file and where they should be placed, then update documentation accordingly.

Written by the indexing model from the issue text.