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.

Sign up for GitHub

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

Jump to bottom

VCF sorting change breaks existing VCFs #1637

Open
lbergelson opened this issue Nov 23, 2022 · 1 comment
Open

VCF sorting change breaks existing VCFs #1637

lbergelson opened this issue Nov 23, 2022 · 1 comment
Assignees
@lbergelson
Labels
bug vcf

Comments

@lbergelson
Copy link
Member

I failed to consider the effect of changing the VCF sort order on processing existing VCFs when merging #1593. This breaks many things.

I think this is still a good idea but we need to reconsider how to do it safely, possibly a split comparator with different levels of sorting vs validating like the sam sort orders use.

The commit e2943b7 reverts #1593.

This blocks #1629 as well.
@lbergelson lbergelson self-assigned this Nov 23, 2022
@lbergelson
Copy link
Member Author

@clintval Sorry, I rolled your change back for now. I'd like to get it back in but it might take me a bit to get to it.

@lbergelson lbergelson mentioned this issue Nov 23, 2022
Open
@lbergelson lbergelson changed the title VCF sorting change breaks existing VCFS VCF sorting change breaks existing VCFs Nov 23, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@lbergelson lbergelson

Labels
bug vcf
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@lbergelson