pseudo_haps() calls the most common allelic states for each SNP marker group across individuals, before building dummy SNPs for each marker group that mimic the binary vcf format. This is the step which determines the haplotype combinations, and therefore enables several summaries to be returned - as contained in the $Hapfile and preliminary $Indfile and finalised $MGfile, following marker group smoothing. This is an internal function not intended for external use.