Adding more functionalities to the data converter for use with plink

[jonbrenas]

While working on GWAS for EAVES, I have observed that adding some functionalities to biallelic_snps_to_plink would make my life easier. Namely:

1. The current version doesn't store the sex calls in the .fam file and plink complains about that (it can be silenced but it should be easy to add the option to have the correct sex calls)
2. There is no option to provide phenotypes which is kind of an issue for GWAS
3. The names of the files are "hardcoded": they are defined as {region}.{n_snps}.{min_minor_ac}.{max_missing_an}.{thin_offset} which is fine as a default but should be modifiable
4. It requires a n_snp (i.e., it is not optional) which is inconvenient when one wants to use as many SNPs as possible.
5. Not sure it will ever be needed but we could also let the user provide a family tree (in what form, I am not sure yet) to fully use the functionality offered by the fam file.
   I will only start working on this if people agree that it makes sense. Feel free to add other ideas and suggestions, if you have any.