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

Move stats calculation to BaseFeatureAdapter #1640

Merged
merged 1 commit into from
Jan 26, 2021
Merged

Conversation

cmdcolin
Copy link
Collaborator

This makes it so that base feature adapter can perform basic local stats calculation, removing the need for adapters like SNPCoverageAdapter, GCContentAdapter, and BigWigAdapter to all implement this independently, and enabling anything that returns a feature score to have this (can also leveraged by FromConfigAdapter in nextstrain demo)

@cmdcolin
Copy link
Collaborator Author

Split out from gwas branch

@github-actions github-actions bot added the needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) label Jan 26, 2021
@codecov
Copy link

codecov bot commented Jan 26, 2021

Codecov Report

Merging #1640 (66547c1) into master (80e4526) will increase coverage by 0.10%.
The diff coverage is 95.40%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #1640      +/-   ##
==========================================
+ Coverage   58.60%   58.70%   +0.10%     
==========================================
  Files         444      445       +1     
  Lines       20385    20378       -7     
  Branches     4787     4792       +5     
==========================================
+ Hits        11946    11963      +17     
+ Misses       8142     8118      -24     
  Partials      297      297              
Impacted Files Coverage Δ
.../sequence/src/GCContentAdapter/GCContentAdapter.ts 1.96% <ø> (+0.64%) ⬆️
...ins/wiggle/src/LinearWiggleDisplay/models/model.ts 75.69% <ø> (ø)
plugins/wiggle/src/index.ts 100.00% <ø> (ø)
plugins/wiggle/src/WiggleRPC/rpcMethods.ts 51.42% <50.00%> (-2.63%) ⬇️
packages/core/util/stats.ts 95.91% <95.91%> (ø)
packages/core/data_adapters/BaseAdapter.ts 62.50% <96.00%> (+17.81%) ⬆️
...ments/src/SNPCoverageAdapter/SNPCoverageAdapter.ts 95.00% <100.00%> (+2.43%) ⬆️
plugins/wiggle/src/BigWigAdapter/BigWigAdapter.ts 96.87% <100.00%> (+2.04%) ⬆️
...inearGenomeView/components/RefNameAutocomplete.tsx 82.75% <0.00%> (-5.18%) ⬇️
plugins/wiggle/src/statsUtil.ts 88.67% <0.00%> (-3.78%) ⬇️
... and 1 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 80e4526...66547c1. Read the comment docs.

@cmdcolin cmdcolin added enhancement New feature or request and removed needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) labels Jan 26, 2021
@rbuels rbuels merged commit d02e5a8 into master Jan 26, 2021
@rbuels rbuels deleted the stats_base_adapter branch January 26, 2021 22:42
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.

2 participants