Using pgen/pvar/psam as LD file

[ariannalandini]

• Possibility to provide pgen/pvar/psam rather than bed/bim/fam as LD reference files (now called bfile), to increase precision using dosages
• If still providing bed/bim/fam, convert anyway in pgen/pvar/psam (with hard calls of course)
• Plink --export option now in use to extarct genotypes and compute LD matrix supports dosages

[ariannalandini]

Implemented in the TileDB input version with commit 24011dd - works only for TileDB input version!
Will need further reworking (e.g. in s01_alpha_sort_alleles_snpid.R, main.nf, etc.) for the summary statistics version.