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 BEDPE add track workflow, avoid showing "Add track" when disabled #3631

Merged
merged 2 commits into from May 18, 2023

Conversation

carolinebridge
Copy link
Contributor

  • adds a track type guess to the bedpe filetype (variant track) such that if you pop it into circular view, it will work
  • follows through with track population if a certain field from the bedpe file is null
  • disables the add track hamburger menu item from the sidebar such that if a user has disabled addtrack it will not give them the option

…l field ;; update disabling track selection to include hamburger menu
@github-actions github-actions bot added the needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) label Apr 6, 2023
@carolinebridge
Copy link
Contributor Author

Should we consider not permitting any track type but VariantTrack on Circular view? I think it's the only one that works on that view, but it goes through the normal add track workflow so there's nothing stopping you from putting in another track type -- and there is currently no error message

@codecov
Copy link

codecov bot commented Apr 6, 2023

Codecov Report

Merging #3631 (2743d46) into main (9a9978b) will increase coverage by 0.00%.
The diff coverage is 41.17%.

@@           Coverage Diff           @@
##             main    #3631   +/-   ##
=======================================
  Coverage   63.06%   63.06%           
=======================================
  Files         871      871           
  Lines       30189    30199   +10     
  Branches     7269     7273    +4     
=======================================
+ Hits        19038    19045    +7     
- Misses      10966    10969    +3     
  Partials      185      185           
Impacted Files Coverage Δ
plugins/bed/src/BedpeAdapter/BedpeAdapter.ts 0.00% <0.00%> (ø)
...ckSelectorWidget/components/tree/HamburgerMenu.tsx 42.85% <40.00%> (+1.68%) ⬆️
plugins/bed/src/index.ts 87.71% <83.33%> (-0.52%) ⬇️

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

(trackTypeGuesser: TrackTypeGuesser) => {
return (adapterName: string) => {
if (adapterName === 'BedpeAdapter') {
return 'VariantTrack'
Copy link
Collaborator

Choose a reason for hiding this comment

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

the choice to make it use VariantTrack may make it unable to use the linear arc display, which may be useful for BEDPE (arc connects the two regions). at one point you mentioned trying to add arc rendering for VariantTrack but that it was tricky. could revisit that perhaps...

Copy link
Collaborator

Choose a reason for hiding this comment

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

more tangential but multi-region arc may be useful too. the LinearAlignmentsArcDisplay ended up becoming multi-region capable recently, and similar concept could apply to the regular LinearArcDisplay

@cmdcolin
Copy link
Collaborator

cmdcolin commented Apr 7, 2023

Should we consider not permitting any track type but VariantTrack on Circular view? I think it's the only one that works on that view, but it goes through the normal add track workflow so there's nothing stopping you from putting in another track type -- and there is currently no error message

this could be interesting. the track selector tries to limit the tracks displayed to ones relevant for a particular view, but add track will let you add anything I think. could be either a 'note/warning' during the add track that it won't apply to current view, or could prohibit. can make issue for this perhaps

@cmdcolin cmdcolin marked this pull request as ready for review May 18, 2023 18:00
@cmdcolin
Copy link
Collaborator

will just go ahead with merge for now. may be good to add some linear arc type display for variant track though

@cmdcolin cmdcolin merged commit 42aa5b3 into main May 18, 2023
9 of 10 checks passed
@cmdcolin cmdcolin changed the title Adds miscellaneous fixes to Add Track workflow Add BEDPE add track workflow, avoid showing "Add track" when disabled May 18, 2023
@cmdcolin cmdcolin added bug Something isn't working enhancement New feature or request and removed needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) labels May 18, 2023
@cmdcolin cmdcolin deleted the small-embed-customizations branch May 18, 2023 18:04
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working enhancement New feature or request
Projects
None yet
Development

Successfully merging this pull request may close these issues.

None yet

2 participants