removal of little-used tools

[brentp]

updates such as my recent effort to move everything to python3 take an amount of time that is super-linear with the amount of code. We have a lot of un-used/little-used tools. I propose that we remove them and make it easier for users to create their own modules as needed to reduce the burden on gemini while improving flexibility.

Here are the current tools: {actionable_mutations,amend,annotate,autosomal_dominant,autosomal_recessive,bcolz_index,browser,burden,comp_hets,db_info,de_novo,dump,examples,fusions,gene_wise,interactions,load,load_chunk,lof_interactions,lof_sieve,mendel_errors,merge_chunks,pathways,qc,query,region,roh,set_somatic,stats,update,windower,x_linked_de_novo,x_linked_dominant,x_linked_recessive

I propose that we remove (in order of my preference to remove).

• [ ] actionable_mutations
• [ ] set_somatic
• [ ] bcolz_index
• [ ] burden
• [ ] fusions
• [ ] interactions
• [ ] stats
• [ ] region
• [ ] lof_seive
• [ ] lof_interactions
• [ ] pathways
• [ ] qc
• [ ] region
• [ ] windower
• [ ] examples

this would leave: {amend,annotate,autosomal_dominant,autosomal_recessive,browser,comp_hets,db_info,de_novo,dump,gene_wise,load,load_chunk,mendel_errors,merge_chunks,pathways,query,roh,update, x_linked_de_novo,x_linked_dominant,x_linked_recessive}

[roryk]

I am down for removing anything you need to make your life easier. AFAIK, the only one of those we use anywhere near non-rarely is --stats.

[brentp]

Hi Rory, thanks for the feedback. is there any particular tool within stats that you use?

[roryk]

Just the simple transversion stats and the genetic distance, something we could easily make a little module for.

[arq5x]

The region tool gets some use and the set_somatic, actionable_mutations, and fusions tools were part of the speedseq paper.

I agree with deprecating these, but perhaps we should start a gemini utilities repo to house the ancillary tools/modules?

[jxchong]

We definitely use region and sometimes stats but stats can be easily replicated with other existing tools.