rewriting format data

Rewriting format data to remove all unnecessary steps that conflict with the community (eg, def at random of funnel codes) + making it compatible with community-curated inputs (genetic maps, physical maps, funnels). All in R.

• manage real strain ID (eg CC001/Unc rather than CC001) x allows to work straight w reference geno info from Broman (w:o reformating)
• append correctly individual ID w strain ID and reformat indiv_geno files so that it copies as many times as replicated in experiment the CCxxx, eg should it is fed w average values (for each CC, one single occurrence) or indiv (for each CC, as many occurrences as phenotyped mice).
• modify crossinfo so that that gets recognized as well....
• test as Rscript passing args
• test w multiple pheno and covar (will require to modify further down/add a step to select the pheno of interest, else that procedure of permutation "homemade" won't work...