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

fix: escaped equal sign in INFO fields #172

Open
wants to merge 1 commit into
base: main
Choose a base branch
from

Conversation

ericblanc20
Copy link

The change made escapes equal sign (=) in INFO fields.

However, the column characters : are also escaped on output, as recommended by the vcf 4.3 format.

It is unclear if the column character : should be escaped in INFO fields of vcf files in 4.2 format. The 4.2 format documentation seems to suggest that only whitespace, semicolons, and equals-sign are forbidden (and therefore should be escaped).

In its current incarnation, vcfpy escapes of column characters regardless of the vcf version. It is unclear to me what is the best practical approach for vcfpy, as I am unsure how strictly commonly used software is following the format.

@ericblanc20 ericblanc20 linked an issue Feb 22, 2024 that may be closed by this pull request
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.

The equal sign is not escaped in output
1 participant