Generalize the "extend-metadata.py" script for any {gene}_coverage columns

[j23414]

Context

For adding {gene}_coverage columns in the ingest pipeline to enable gene specific tree building, it would be useful to generalize the following script to more than RSV "G" and "F" genes.

• ingest/bin/extend-metadata.py

One step towards generalization is instead of hardcoding the "G" and "F" start and end coordinates in the extend-metadata.py script,

• move the coordinates to the "configfile.yaml" to be passed in as arguments
• or refactor this script to capture the coordinates from the A or B reference genbank files.

Related Discussion

• https://github.com/nextstrain/private/issues/102#issuecomment-1998319552
• Add E gene trees dengue#18

Examples

Possible solution

[rneher]

commit 2d9a606 uses nextclade cdsCoverage to deduce coverage. this can be readily generalized to any gene (and the Nextclade output currently persists in the metadata file).