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Display VCF filters as QC bages in scout cancer

See original GitHub issue

I was going to add the annotated VCF filters as badges for the cancer variants list view.

Scout stores these flags as “filters” in the database and are included in the variant_obj.

We would like to apply different formatting to these flags in a way that would be extendable and meaningful for different sites. I was therefore thinking of storing the configuration in the scout database, much like how we do with the dismissal terms.

What do you think?

Issue Analytics

State:
Created 2 years ago
Comments:12 (7 by maintainers)

Top GitHub Comments

1reaction

mhkccommented, Jun 24, 2021

Wouldnt that soon become bloated and hard to manage? Especially if different sites are to have different prefixes. Then it would be better to let the formatting be defined in the config.py or to load the configuration into the database.

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mhkccommented, Jun 24, 2021

Not having these in the constants file doesn’t mean that there are no defaults. We could either have a defaults json file which are being loaded when the database is being setup (just like the evaluation terms), or just have a default dictionary in the config file.

I do think we should strive to unify as much as possible but it seems to me that is a process that takes a lot of time to mature.

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