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

Add better handling for bedMethyl files #4662

Merged
merged 4 commits into from
Nov 18, 2024
Merged

Add better handling for bedMethyl files #4662

merged 4 commits into from
Nov 18, 2024

Conversation

cmdcolin
Copy link
Collaborator

Our default bedMethyl parser would get confused by these, and think it was UCSC transcript. It is hard to really tell what data in a BED file is indicating without any header. We try to use heuristics to determine when something should be a UCSC transcript in BED format but it is tricky. In any case, this PR adds more heuristics to detect bedMethyl, parse it in a specialized way

This PR also makes it so that they can be displayed in a MultiQuantitativeTrack. This lets you split out the modifications types into different subtracts. This requires passing the currently displayed regions to the "getSources" wiggle RPC call. there were older comments that said it would do this but now it just does it :)

image

@cmdcolin
Copy link
Collaborator Author

fixes #3842

@cmdcolin cmdcolin merged commit a439fd6 into main Nov 18, 2024
4 checks passed
@cmdcolin cmdcolin deleted the bedmethyl branch November 18, 2024 16:57
@cmdcolin cmdcolin added the enhancement New feature or request label Nov 18, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

Successfully merging this pull request may close these issues.

1 participant