cmd/check-sort-order/ takes a genome file and (currently) a .vcf.gz or a .bed.gz and
checks that:
- a .tbi is present
- the VCF has ""##fileformat=VCF" as the first line
- the VCF has a #CHROM header
- the chromosome are in the order specified by the genome file (and present)
- the positions are sorted
- the positions are <= the chromosome lengths defined in the genome file.
As a result, any new genome going into GGD will have a .genome file that will dictate the sort order and presence or absence of the 'chr' prefix for chromosomes.