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Fix drawing inverted CIGAR segments on dotplot #3170

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merged 7 commits into from
Sep 7, 2022

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cmdcolin
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@cmdcolin cmdcolin commented Sep 4, 2022

Example link
http://jbrowse.org/code/jb2/fix_inverted_cigar_dotplot/?config=test_data%2Fconfig_dotplot.json&session=share-6ilxWDe7Ts&password=DQxxV

Note the top view actually has query and target backwards (and produces warnings), and the bottom one has it right (and has no warnings)

@github-actions github-actions bot added the needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) label Sep 4, 2022
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codecov bot commented Sep 4, 2022

Codecov Report

Merging #3170 (4ced53f) into main (7ed81c2) will increase coverage by 0.04%.
The diff coverage is 73.33%.

@@            Coverage Diff             @@
##             main    #3170      +/-   ##
==========================================
+ Coverage   59.45%   59.50%   +0.04%     
==========================================
  Files         671      671              
  Lines       28628    28633       +5     
  Branches     6926     6927       +1     
==========================================
+ Hits        17022    17039      +17     
+ Misses      11284    11272      -12     
  Partials      322      322              
Impacted Files Coverage Δ
...otplot-view/src/DotplotRenderer/DotplotRenderer.ts 77.21% <42.85%> (+2.53%) ⬆️
...s/breakpoint-split-view/src/BreakpointSplitView.ts 71.69% <100.00%> (ø)
...breakpoint-split-view/src/components/Breakends.tsx 88.09% <100.00%> (ø)
products/jbrowse-web/src/tests/util.tsx 93.93% <100.00%> (+0.09%) ⬆️
plugins/hic/src/HicRenderer/HicRenderer.tsx 95.45% <0.00%> (-4.55%) ⬇️
...lot-view/src/DotplotView/components/ImportForm.tsx 67.53% <0.00%> (ø)
packages/core/util/layouts/GranularRectLayout.ts 87.28% <0.00%> (+0.42%) ⬆️
...FeatureRenderer/components/ProcessedTranscript.tsx 88.73% <0.00%> (+1.40%) ⬆️
packages/core/util/Base1DUtils.ts 97.00% <0.00%> (+2.00%) ⬆️
...rarchicalTrackSelectorWidget/components/Header.tsx 43.47% <0.00%> (+2.17%) ⬆️
... and 4 more

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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 Sep 6, 2022
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cmdcolin commented Sep 7, 2022

added a canvas-snapshot integration test for drawing an inverted alignment now

also went through and typescript-ified a bunch of the integration tests

@cmdcolin cmdcolin merged commit 1b125fe into main Sep 7, 2022
@cmdcolin cmdcolin deleted the fix_inverted_cigar_dotplot branch September 7, 2022 21:40
cmdcolin added a commit that referenced this pull request Sep 14, 2022
* Fix drawing inverted segments on dotplot renderer

* Accomodate undefined MatePosition

* Typescriptify test

* More typescripting

* Gzip + CIGAR gzip

* More typescripting

* More typescripting
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