nextstrain/seasonal-flu

CDS coordinates are incorrect for Vic and Yam hemagglutinin

huddlej opened this issue · 1 comments

Current Behavior

@kistlerk noticed that the demarcated region for HA1 is not divisible by 3 in the HA reference files for Vic and Yam.

Expected behavior

The CDS for HA1 should say 57..1094 rather than 1095 and SigPep should be 12..56.

CDS coordinates in GenBank format are 1-based and closed. To calculate the amino acids in a given range, you have to add 1 to the range before dividing by 3. For H3N2's HA, we get the 16 amino acids of SigPep by (48 - 1 + 1) / 3 and the 329 of HA1 with (1035 - 49 + 1) / 3.

From Slack conversation, coordinates for Vic was fixed but not Yam (yet)

Edit: Yam's coordinates were also corrected during the refactoring of the workflow (~June 2022). We just haven't run a Yam build since 2021-12-11...