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poseidon-framework / poseidon-hs

A toolset to work with modular genotype databases in the Poseidon format
https://poseidon-framework.github.io/#/trident
MIT License
7 stars 2 forks source link

janno contamination consistency ignores NA #270

Closed stschiff closed 1 year ago

stschiff commented 1 year ago

The current implementation complains if NA is in the Contamination column, with no values in the two other required Contamination fields. That is obviously a bug, because the specification makes no semantic difference between an empty string and NA.

nevrome commented 1 year ago

Hm... I can not reproduce this. How exactly did you encode NA? Literally with NA or with the correct n/a? Maybe that's already the issue? Or how could I reproduce this behaviour?

Independent of that we should certainly improve the validation for these sets of columns. We already discussed this in #153 and I still think that's the right way to approach this. Also considering semantic changes we may want to apply to the schema (https://github.com/poseidon-framework/poseidon-schema/issues/64).

stschiff commented 1 year ago

Yeah, very sorry to have wasted your time 🙈, I used NA. Good learning session for me. I'll close this.