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Fix ability to search and load data files using lower case refName aliases #3041

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merged 7 commits into from
Jun 21, 2022

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cmdcolin
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Currently, you can query for lower case ref names such as e.g. ctga:1-100 on volvox, but with refnamealiases it does not work. E.g. contiga:1-100 fails

This fixes it so that you can use lower case naming in the refname autocomplete for searching

Small amount of other refactoring code in PR, and adding chrMT to hg19 refname aliases

@github-actions github-actions bot added the needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) label Jun 16, 2022
@cmdcolin cmdcolin changed the title Fix lower case refnamealiases Fix ability to search for lower case chromosome names that are ref name aliases Jun 16, 2022
@cmdcolin cmdcolin removed the needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) label Jun 16, 2022
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Fixes #3039

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codecov bot commented Jun 16, 2022

Codecov Report

Merging #3041 (8d1f8a0) into main (08c8111) will increase coverage by 0.08%.
The diff coverage is 91.42%.

@@            Coverage Diff             @@
##             main    #3041      +/-   ##
==========================================
+ Coverage   61.70%   61.78%   +0.08%     
==========================================
  Files         590      590              
  Lines       26915    26912       -3     
  Branches     6526     6525       -1     
==========================================
+ Hits        16607    16627      +20     
+ Misses      10005     9982      -23     
  Partials      303      303              
Impacted Files Coverage Δ
...inearGenomeView/components/SearchResultsDialog.tsx 71.69% <ø> (+22.64%) ⬆️
...view/src/LinearGenomeView/components/SearchBox.tsx 86.84% <50.00%> (-0.40%) ⬇️
packages/core/assemblyManager/assemblyManager.ts 71.62% <87.50%> (ø)
...enome-view/src/LinearGenomeView/components/util.ts 85.71% <90.00%> (+10.71%) ⬆️
packages/core/assemblyManager/assembly.ts 92.25% <100.00%> (+0.88%) ⬆️
...fig/src/RefNameAliasAdapter/RefNameAliasAdapter.ts 92.30% <100.00%> (ø)
...iew/src/LinearGenomeView/components/ImportForm.tsx 78.37% <100.00%> (+0.60%) ⬆️
.../linear-genome-view/src/LinearGenomeView/index.tsx 84.61% <0.00%> (-0.34%) ⬇️
products/jbrowse-web/src/util.ts 27.27% <0.00%> (ø)
products/jbrowse-cli/src/commands/text-index.ts 70.62% <0.00%> (+1.39%) ⬆️
... and 5 more

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@cmdcolin cmdcolin force-pushed the fix_lowercase_refnamealiases branch from fff0e08 to 68ea203 Compare June 16, 2022 20:39
@github-actions github-actions bot added the needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) label Jun 16, 2022
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this doesn't support queries like chrmt:1-100, but it could be a starter

@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 Jun 17, 2022
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allows lowercase locstrings now, and also allows data files with either Chr1 or chr1. various tests added also to try to cover these cases, with a bit of refactoring to help the import form's search box to use the same fetchResults utility as the lgv header search box

@cmdcolin cmdcolin force-pushed the fix_lowercase_refnamealiases branch from 2126af2 to 8d1f8a0 Compare June 17, 2022 15:07
@cmdcolin cmdcolin merged commit cd1cd08 into main Jun 21, 2022
@cmdcolin cmdcolin deleted the fix_lowercase_refnamealiases branch June 21, 2022 15:14
@cmdcolin cmdcolin changed the title Fix ability to search for lower case chromosome names that are ref name aliases Fix ability to search and load data files using lower case refName aliases Jun 21, 2022
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