Should we use -R {reference/representative} in call to ncbi-genome-download?

[kbshimmyo]

Note also Ben's lunchtime verbal comment of cutting down magicblast-against-"bacteria" [or other large db] to look only at representative bacterial genomes (instead of all) as a coarse-grained option.

This would involve identifying whether taxList argument is a group-level identifier or a quoted flag for ncbi-genome-download - hacky poorly-validated distinction could be based on whether the first char of taxList is a dash.

[kbshimmyo]

Based on talking to Bastian, changing to use -R representative in calls to genome downloader (in my branch! not master yet)

This wasn't a good idea: for granular taxlist (like a taxid), the genome downloader doesn't find anything to download.

Suggestion:
if the taxList is a group [by whatever hacky criterion], do -R representative call.
otherwise, no -R flag.

[kbshimmyo]

To be clear, we are currently not using -R representative at all.