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Fix allRefNames on assembly #1390

Merged
merged 2 commits into from Nov 3, 2020
Merged

Fix allRefNames on assembly #1390

merged 2 commits into from Nov 3, 2020

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garrettjstevens
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Restores previous functionality to return a list of all refNames and aliases.

@garrettjstevens garrettjstevens self-assigned this Nov 3, 2020
@garrettjstevens garrettjstevens added this to To do in JBrowse team board via automation Nov 3, 2020
@garrettjstevens garrettjstevens moved this from To do to In progress in JBrowse team board Nov 3, 2020
aliases = aliases.concat(aliasList)
const aliases: string[] = []
self.refNameAliases.forEach((_canonicalName, alias) => {
if (this.refNames && !this.refNames.includes(alias)) {
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refNameAliases contains the canonical refNames so should be able to return keys of refNameAliases only

@rbuels
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rbuels commented Nov 3, 2020

what was the motivation for this? what problem was cropping up?

@garrettjstevens
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This was the problem that originally caused the bug fixed by #1386. I realized that when reviewing #1386.

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codecov bot commented Nov 3, 2020

Codecov Report

Merging #1390 into master will decrease coverage by 0.03%.
The diff coverage is 0.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #1390      +/-   ##
==========================================
- Coverage   59.38%   59.34%   -0.04%     
==========================================
  Files         418      418              
  Lines       18683    18684       +1     
  Branches     4404     4405       +1     
==========================================
- Hits        11094    11088       -6     
- Misses       7294     7301       +7     
  Partials      295      295              
Impacted Files Coverage Δ
packages/core/assemblyManager/assembly.ts 81.30% <0.00%> (-0.67%) ⬇️
...s/svg/src/SvgFeatureRenderer/components/Chevron.js 85.00% <0.00%> (-10.00%) ⬇️
...lignments/src/BamAdapter/BamSlightlyLazyFeature.ts 77.35% <0.00%> (-1.89%) ⬇️

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@cmdcolin cmdcolin merged commit 7fff8db into master Nov 3, 2020
JBrowse team board automation moved this from In progress to Done Nov 3, 2020
@cmdcolin cmdcolin deleted the fix_allrefnames branch March 19, 2021 15:03
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3 participants