Lineage P.1 has 17 SNPs in note field, but only 16 in csv output

[pmenzel]

Hi,

the file variants_p1.csv has 16 columns with SNPs for the P.1 variant:

query,ref_count,alt_count,other_count,fraction_alt,aa:orf1ab:S1188L,aa:orf1ab:K1795Q,del:11288:9,aa:S:L18F,aa:S:T20N,aa:S:P26S,aa:S:D138Y,aa:S:R190S,aa:S:K417T,aa:S:E484K,aa:S:N501Y,aa:S:H655Y,aa:S:T1027I,aa:orf3a:G174C,aa:orf8:E92K,aa:N:P80R

whereas the note column in the report.csv shows x/17 detected SNPs for this lineage, probably because of the hard-coded 17 here:

pangolin/pangolin/scripts/pangolearn.smk

Line 307 in 8bdd935

note = f'{snps["alt"]}/17 P.1 (B.1.1.28.1) SNPs ({snps["ref"]} ref and {snps["oth"]} other)'

[aineniamh]

Hi @pmenzel, thanks for catching that! I've updated it in the master now and the next release will have the changes incorporated.

[whottel]

Similar to the issue originally mentioned here.
pangolearn.smk sets the denominator for P.1 to 16 even though there are only 15 listed in config_p.1.csv