Skip to content

alt_alleles dimension is not picked up when max_number is zero #359

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
tomwhite opened this issue Apr 22, 2025 · 0 comments · May be fixed by #360
Open

alt_alleles dimension is not picked up when max_number is zero #359

tomwhite opened this issue Apr 22, 2025 · 0 comments · May be fixed by #360
Labels
bug Something isn't working

Comments

@tomwhite
Copy link
Contributor

Found while working on sgkit-dev/vcztools#198

Note that the Number=A becomes Number=1 in the following conversion:

$ bcftools view --header-only tests/data/vcf/1kg_2020_chr20_annotations.bcf | grep HWE_EUR_unrel
##INFO=<ID=HWE_EUR_unrel,Number=A,Type=Float,Description="HWE test in EUR (2504 unrelated samples) (PMID:15789306); 1=good, 0=bad">
$ vcf2zarr convert --force tests/data/vcf/1kg_2020_chr20_annotations.bcf 1kg_2020_chr20_annotations.vcz
$ vcztools view --header-only 1kg_2020_chr20_annotations.vcz | grep HWE_EUR_unrel
##INFO=<ID=HWE_EUR_unrel,Number=1,Type=Float,Description="HWE test in EUR (2504 unrelated samples) (PMID:15789306); 1=good, 0=bad">

This is similar on the surface to #353, but there's a deeper problem to do with handling the case where the VCF header declares Number=A, but the max_number found when writing the ICF is 0.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working
Projects
None yet
Development

Successfully merging a pull request may close this issue.

1 participant