Comments (3)
kmoad
commented on June 9, 2024
Thanks for the feedback. I agree that this is annoying. We've added it to our bug tracker to ignore dicts where all the values are None.
While we wait for the next version though. It's possible to solve this for each of the modules you're having trouble with. Could you send a list?
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EugeneEA
commented on June 9, 2024
Awesome, also I can easily wait for the new release.
We've added it to our bug tracker to ignore dicts where all the values are None.
So you are planning to change all annotators to return empty list if no data present?
I'm currently working with following annotators:
gerp, interpro, repeat, clinvar, esp6500, gnomad3, thousandgenomes
From these Clinvar and esp6500 returns empty lists and the rest list of Nones.
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kmoad
commented on June 9, 2024
We've updated gerp, interpro, repeat, gnomad3, and thousandgenomes so that they will be an empty list in secondary_data. You can get the new versions with oc module update. Let me know if it works!
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Related Issues (20)
- UniProt HOT 2
- Error in IGV widget HOT 1
- pharmgkb OC and website differing annotations HOT 7
- gnomad update HOT 1
- Variant Conversion HOT 3
- rdata download option not working HOT 1
- silent failures from multiple annotators HOT 2
- Support for Spanning or overlapping deletions HOT 1
- Access to error logs from web server HOT 1
- Homozygous reference variants HOT 1
- KeyError in sample_id with multiple VCF files HOT 1
- New databases creation HOT 4
- Single variant tab not working! HOT 2
- python 3.12 module imp deprecated HOT 1
- Ambiguous annotation results HOT 1
- incorrect SO assignment - "exon_loss_variant" for intronic region
- IndexError: index out of range when annotating vcf file HOT 1
- How to update Open-CRAVAT from v2.2.9 to v2.5.0 ? HOT 1
- Update link in OC versions <v2.5 is unreadable and unusable HOT 1
- oc module install-base issue HOT 2
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