Taxon threshold default values in code

[martinghunt]

Noting this for future in case we get bugs/want to change...

Ideally, these would be in the data download, not the code:

mykrobe/src/mykrobe/metagenomics/phylo.py

Lines 12 to 25 in 9560b30

	DEFAULT_THRESHOLD = 30
	TAXON_THRESHOLDS = {
	"Saureus" : 30,
	"Sepidermidis" : 30,
	"Shaemolyticus" : 30,
	"Sother" : 15,
	"Coagneg" : 30,
	"Staphaureus" : 30,
	"Escherichia_coli" : 15,
	"Klebsiella_pneumoniae" : 15,
	"Ecoli_Shigella": 90,
	"Shigella_sonnei": 90,
	}

(was easy to put them here when ref data got rewritten to live on figshare, but is not ideal)

Not sure if the defaults of 90 will be ok for shigella - see if we get bug reports.