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Add ability to load all built-in synteny data sources from @jbrowse/cli #3574

Merged
merged 4 commits into from
Mar 13, 2023
Merged

Add ability to load all built-in synteny data sources from @jbrowse/cli #3574

merged 4 commits into from
Mar 13, 2023

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cmdcolin
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@cmdcolin cmdcolin commented Mar 13, 2023 •
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Adds

  • liftover chain
  • delta (mummer)
  • out (mashmap)
  • mcscan anchors+simpleanchors

fixes #2816

@github-actions github-actions bot added the needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) label Mar 13, 2023
@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 Mar 13, 2023
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codecov bot commented Mar 13, 2023

Codecov Report

Merging #3574 (bff19cd) into main (ce05d01) will increase coverage by 0.14%.
The diff coverage is 89.58%.

@@            Coverage Diff             @@
##             main    #3574      +/-   ##
==========================================
+ Coverage   62.70%   62.84%   +0.14%     
==========================================
  Files         866      866              
  Lines       30279    30269      -10     
  Branches     7290     7292       +2     
==========================================
+ Hits        18986    19023      +37     
+ Misses      11104    11057      -47     
  Partials      189      189
Impacted Files Coverage Δ
products/jbrowse-cli/src/commands/add-track.ts 83.09% <89.58%> (+20.87%) ⬆️

... and 1 file with indirect coverage changes

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

@cmdcolin cmdcolin changed the title Add ability to load more all built in synteny data sources from command line Add ability to load all built-in synteny data sources from @jbrowse/cli Mar 13, 2023
@cmdcolin cmdcolin merged commit eee0fe1 into main Mar 13, 2023
@cmdcolin cmdcolin deleted the synteny_command_line branch March 13, 2023 20:21
@cmdcolin cmdcolin mentioned this pull request Mar 14, 2023
Merged
cmdcolin added a commit that referenced this pull request May 18, 2023
@cmdcolin
Add ability to load all built-in synteny data sources from @jbrowse/c…
46d9acb 
…li (#3574)

* Bump yarn.lock

* Add PAF test

* Add more functionality for loading synteny on the command line

* Bump deps
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Add ability to load more syntenytrack formats in the CLI
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