Skip to content
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

Type error prevents SV filtration #1743

Closed
holtgrewe opened this issue Jun 26, 2024 · 0 comments · Fixed by #1744
Closed

Type error prevents SV filtration #1743

holtgrewe opened this issue Jun 26, 2024 · 0 comments · Fixed by #1744
Labels
bug Something isn't working

Comments

@holtgrewe
Copy link
Collaborator

Describe the bug
When writing out the VCF for the SV filtration in the worker, VarFish may write out floats for integer FORMAT fields. This leads to an error in parsing with recent noodles-vcf versions.

To Reproduce
See row ending in

GT:cn:GQ        1/1:0.03:17

The corresponding header line is

##FORMAT=<ID=cn,Number=1,Type=Integer,Description="Copy number of the variant in the sample">

Expected behavior
Coerce value to int.

Additional context
N/A

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
Archived in project
Development

Successfully merging a pull request may close this issue.

1 participant