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Fix potential crashes where alignment SEQ field may be empty, simplify some display model code #3620

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merged 2 commits into from
Apr 4, 2023

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@cmdcolin cmdcolin commented Apr 3, 2023

SEQ is often left empty on secondary alignments, and this causes at least one error in our code (per-base coloring on alignments tracks)

This adds typescript notes that feature.get('SEQ') returns string|undefined and fixes related issues

@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 3, 2023
@cmdcolin cmdcolin force-pushed the fix_secondary_perbase branch 2 times, most recently from 070a18b to f4d9e2e Compare April 3, 2023 19:06
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codecov bot commented Apr 3, 2023

Codecov Report

Merging #3620 (de6571f) into main (9fe2420) will decrease coverage by 0.02%.
The diff coverage is 19.23%.

@@            Coverage Diff             @@
##             main    #3620      +/-   ##
==========================================
- Coverage   62.96%   62.94%   -0.02%     
==========================================
  Files         871      871              
  Lines       30193    30199       +6     
  Branches     7271     7271              
==========================================
- Hits        19012    19010       -2     
- Misses      10996    11003       +7     
- Partials      185      186       +1     
Impacted Files Coverage Δ
packages/core/ReExports/modules.tsx 11.16% <ø> (ø)
...rc/LinearPileupDisplay/components/SetMaxHeight.tsx 0.00% <0.00%> (ø)
...nts/src/SNPCoverageAdapter/generateCoverageBins.ts 50.84% <0.00%> (-0.88%) ⬇️
...ns/alignments/src/PileupRenderer/PileupRenderer.ts 51.80% <18.18%> (-0.64%) ⬇️
...lugins/alignments/src/LinearPileupDisplay/model.ts 66.25% <50.00%> (-0.14%) ⬇️
...ative-view/src/LinearReadVsRef/LinearReadVsRef.tsx 74.22% <100.00%> (ø)
...ns/wiggle/src/LinearWiggleDisplay/models/model.tsx 72.07% <100.00%> (-0.38%) ⬇️

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@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 Apr 4, 2023
@cmdcolin cmdcolin merged commit b7504be into main Apr 4, 2023
@cmdcolin cmdcolin changed the title Fix potential crashes where alignment SEQ field may be empty Fix potential crashes where alignment SEQ field may be empty, simplify some display model code Apr 4, 2023
@cmdcolin cmdcolin deleted the fix_secondary_perbase branch April 4, 2023 21:10
cmdcolin added a commit that referenced this pull request May 18, 2023
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