Since the design of the chunks depends only on (1) the representative genomes / the pan-genome (2) chunk size. We decide to cache the chunk's design. Besides, in addition to carry the chunks design in a global variable, which can be quite heavy for large number of species of interest, we decide to only carry the cache path of the chunks for given species.
Add major/minor allele compute to midas_run_snps, and the user can choose to report extra columns by --advanced.
Clean up commands to build midas db while building it for GTDB.
Add midasdb_name and get_midasdb_layout to accesss to any path that is related with midas database.
Update unit testing codes, as well as building toy db locally.
midas_run_snps, and the user can choose to report extra columns by--advanced.midasdb_nameandget_midasdb_layoutto accesss to any path that is related with midas database.