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Collapse introns #4033

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@cmdcolin cmdcolin commented Nov 2, 2023

This is a work in progress for collapsing introns in the linear genome view

Very basic implementation, filtering exon subfeatures and adds a small window around each exon, and creates a list of displayedRegions from that

fixes #557

@github-actions github-actions bot added the needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) label Nov 2, 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 Nov 2, 2023
@cmdcolin cmdcolin added the size large pretty big label Nov 22, 2023
@cmdcolin cmdcolin marked this pull request as draft November 22, 2023 16:42
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it was mentioned recently that this could be made an external plugin while the details of this are getting resolved. there are some tricky issues but if it's external, little lower bar for acceptance

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codecov bot commented Mar 12, 2024

Codecov Report

Attention: Patch coverage is 0% with 19 lines in your changes missing coverage. Please review.

Project coverage is 62.53%. Comparing base (a097560) to head (9158297).
Report is 132 commits behind head on main.

Current head 9158297 differs from pull request most recent head 5c93cdc

Please upload reports for the commit 5c93cdc to get more accurate results.

Files Patch % Lines
...aseLinearDisplay/models/BaseLinearDisplayModel.tsx 0.00% 18 Missing ⚠️
...earPileupDisplay/SharedLinearPileupDisplayMixin.ts 0.00% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #4033      +/-   ##
==========================================
- Coverage   62.61%   62.53%   -0.08%     
==========================================
  Files        1088     1088              
  Lines       31495    31518      +23     
  Branches     7531     7532       +1     
==========================================
- Hits        19721    19711      -10     
- Misses      11602    11632      +30     
- Partials      172      175       +3     

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Misc

Update snaps

Collapse intron p1

Properly size linear genome view after creation

Bump deps
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Create method to collapse introns in LGV
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