Merge pull request #7 from camillescott/ejb_master

Change structure of mutation positions to be more sane
add beginning plan for gene mut tally in simulated data
no changes, really
update readme since JBarrick/OTenaillon mtg

delete proc3, ask a question for each procedure, delete mutation implementation notes
formatting correction
more edit
remove old proc3, adjust accordingly
Functions for writing out gene count results, changed gene frequencies to use loguc_tag instead of gene name