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

Remove vcf_header option from write_vcf #47

Closed
jeromekelleher opened this issue Aug 6, 2024 · 1 comment · Fixed by #86
Closed

Remove vcf_header option from write_vcf #47

jeromekelleher opened this issue Aug 6, 2024 · 1 comment · Fixed by #86

Comments

@jeromekelleher
Copy link
Contributor

vcztools view needs to produce the appropriate header in all situations, and having an input header as an option is not really very helpful. We need to subset the samples and fields in all sorts of ways, and parsing the source header here is not the right approach. Header parsing should be done in bio2zarr.

Note that do this fully, we will need to update the VCF Zarr specification and vcf2zarr in order to store sufficient information about the header, rather than the header itself. This will require some coordinated updates across repos.

I think the simplest approach here is to just delete the option for proving a complete header here, and see what we're missing.

See:

@jeromekelleher
Copy link
Contributor Author

See the linked issues in sgkit-dev/vcf-zarr-spec#15 (comment) for notes on how we might avoid storing the full header, and retain lossless encoding of the information in it.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging a pull request may close this issue.

1 participant