Instead of providing genome (-g) files, have chrom_sizes for several widely-used genomes burned into the tool.
Obvious issue is chromosome naming schemes. Could have:
'hg19' [chr1, chr2, ...]
'hg19-int' [1, 2, ...]
Possibly dangerous however, as the advantage of the -g file approach is that the user KNOWS what they are doing, whereas under this model, results could be wrong owing to unknown differences in the chrom naming schemes (e.g., the 7,459 ways that the mitochondria is named)
Instead of providing genome (-g) files, have chrom_sizes for several widely-used genomes burned into the tool.
Obvious issue is chromosome naming schemes. Could have:
Possibly dangerous however, as the advantage of the -g file approach is that the user KNOWS what they are doing, whereas under this model, results could be wrong owing to unknown differences in the chrom naming schemes (e.g., the 7,459 ways that the mitochondria is named)