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Display more informative flash messages when a panel creation from file fails

See original GitHub issue

A user was trying to create a new gene panel but couldn’t (displayed message was a generic “something went wrong in creating the panel”). With @moahaegglund we found out that it was because two genes in the panel file are missing in scout database:

HLA-DRB3(4951)
HLA-DRB4(4952)

It would be useful that instead of getting the generic error message the user could know what went wrong in the upload. For instance the scout log displays clearly: WARNING hgnc_id 4951 is not in the gene database! WARNING hgnc_id 4952 is not in the gene database!

Question, why are not these 2 genes in our database?

Issue Analytics

State:
Created 4 years ago
Reactions:1
Comments:8 (1 by maintainers)

Top GitHub Comments

1reaction

dnilcommented, Feb 25, 2020

As the gene is not in the db being on 6, but rather on GL000255, it will not be fetched, loaded, parsed or searchable in the scout db…

0reactions

henrikstranneheimcommented, Feb 25, 2020

MIP will use alternative contigs in the mapping, but only use primary contigs downstream of this. So any variants in the alternative contigs will not make it to Scout

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