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

.vcf.bgz as a valid vcf extension in FileExtensions #1727

Merged
merged 2 commits into from
Oct 29, 2024

Conversation

lindenb
Copy link
Contributor

@lindenb lindenb commented Oct 29, 2024

Description

VCF suppliers like gnomad, provide VCF with the vcf.bgz extension (eg https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/vcf/exomes/gnomad.exomes.v4.1.sites.chr1.vcf.bgz ) . This PR adds vcf.bgz as a valid extension, defined as COMPRESSED_VCF_BGZ

Things to think about before submitting:

  • Make sure your changes compile and new tests pass locally.
  • Add new tests or update existing ones:
    • A bug fix should include a test that previously would have failed and passes now.
    • New features should come with new tests that exercise and validate the new functionality.
  • Extended the README / documentation, if necessary
  • Check your code style.
  • Write a clear commit title and message
    • The commit message should describe what changed and is targeted at htsjdk developers
    • Breaking changes should be mentioned in the commit message.

@lindenb lindenb marked this pull request as ready for review October 29, 2024 14:04
Copy link
Member

@lbergelson lbergelson left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

👍 Looks like an improvement to me. My only comment is that we might want to make it a method "hasCompressedVcfExtension()" or something like that. We can always revisit that in the future though.

@lbergelson lbergelson merged commit 4ea3285 into samtools:master Oct 29, 2024
4 checks passed
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 this pull request may close these issues.

2 participants