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Fix rendering base-level alignments on synteny visualizations, especially in inverted regions #3419

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merged 25 commits into from
Dec 20, 2022

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cmdcolin
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  • Gets rid of the awkward flipInsDel variable on the synteny feature, instead, properly fixing the CIGAR string in the adapter
  • Gets rid of the awkward revCigar variable on the synteny feature, instead, properly fixing the CIGAR string in the adapter
  • Adds mutated-volvox example with some CIGARs and indels and inversions. I visually verify all the indels inside of inversions and add unit tests to help catch this

@github-actions github-actions bot added the needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) label Dec 19, 2022
@cmdcolin cmdcolin added bug Something isn't working and removed needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) labels Dec 19, 2022
@cmdcolin cmdcolin force-pushed the fix_cigar_reversing branch from 99c8750 to 72b7a31 Compare December 19, 2022 23:49
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codecov bot commented Dec 19, 2022

Codecov Report

Merging #3419 (4e4a512) into main (a4e9f67) will decrease coverage by 0.00%.
The diff coverage is 67.02%.

@@            Coverage Diff             @@
##             main    #3419      +/-   ##
==========================================
- Coverage   61.35%   61.35%   -0.01%     
==========================================
  Files         818      822       +4     
  Lines       29526    29534       +8     
  Branches     7098     7087      -11     
==========================================
+ Hits        18117    18120       +3     
- Misses      11239    11244       +5     
  Partials      170      170              
Impacted Files Coverage Δ
...plotView/components/ImportSyntenyTrackSelector.tsx 4.16% <ø> (ø)
...ve-view/src/LGVSyntenyDisplay/stateModelFactory.ts 3.89% <0.00%> (-0.22%) ⬇️
...tenyView/components/ImportSyntenyTrackSelector.tsx 4.16% <ø> (ø)
...ar-comparative-view/src/LinearSyntenyView/model.ts 75.00% <33.33%> (ø)
...lugins/comparative-adapters/src/PAFAdapter/util.ts 39.68% <39.68%> (ø)
...parative-adapters/src/PAFAdapter/SyntenyFeature.ts 80.00% <80.00%> (ø)
...-view/src/LinearSyntenyRenderer/components/util.ts 82.27% <82.27%> (ø)
.../comparative-adapters/src/PAFAdapter/PAFAdapter.ts 88.23% <90.90%> (+24.87%) ⬆️
...otplot-view/src/DotplotRenderer/DotplotRenderer.ts 77.21% <100.00%> (-0.97%) ⬇️
...tenyRenderer/components/LinearSyntenyRendering.tsx 60.13% <100.00%> (-6.11%) ⬇️
... and 4 more

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@cmdcolin cmdcolin force-pushed the fix_cigar_reversing branch from 72b7a31 to 7aa78cd Compare December 19, 2022 23:58
@cmdcolin cmdcolin force-pushed the fix_cigar_reversing branch from 7aa78cd to c1f1460 Compare December 20, 2022 02:53
@cmdcolin cmdcolin force-pushed the fix_cigar_reversing branch from c1f1460 to 4e4a512 Compare December 20, 2022 03:45
@cmdcolin cmdcolin merged commit 3f29635 into main Dec 20, 2022
@cmdcolin cmdcolin deleted the fix_cigar_reversing branch December 20, 2022 04:43
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