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Add ability to get stitched together CDS, protein, and cDNA sequences in feature details #1758

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merged 14 commits into from
Mar 4, 2021

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@cmdcolin cmdcolin commented Mar 3, 2021

Requested by #1755

Example screenshot:

localhost_3000__config=test_data%2Fconfig json session=local-Jn6bNBkPk

There are more things that could be done including getting promoter/intron sequences (add +/- some user-configurable number of bases) around the region, but I think this is possibly a good start

@github-actions github-actions bot added the needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) label Mar 3, 2021
@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 Mar 3, 2021
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codecov bot commented Mar 3, 2021

Codecov Report

Merging #1758 (7966a19) into master (a1ae57d) will decrease coverage by 0.19%.
The diff coverage is 30.21%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #1758      +/-   ##
==========================================
- Coverage   58.74%   58.54%   -0.20%     
==========================================
  Files         455      455              
  Lines       21049    21140      +91     
  Branches     4987     5011      +24     
==========================================
+ Hits        12365    12377      +12     
- Misses       8375     8453      +78     
- Partials      309      310       +1     
Impacted Files Coverage Δ
...lignmentsFeatureDetail/AlignmentsFeatureDetail.tsx 41.79% <ø> (ø)
...archicalTrackSelectorWidget/components/Category.js 86.66% <ø> (ø)
...src/LinearGenomeView/components/SequenceDialog.tsx 48.71% <ø> (ø)
...quenceRenderer/components/DivSequenceRendering.tsx 93.25% <ø> (-1.34%) ⬇️
.../src/VariantFeatureWidget/VariantFeatureWidget.tsx 45.20% <ø> (ø)
products/jbrowse-web/src/jbrowseModel.js 65.85% <ø> (ø)
...kages/core/BaseFeatureWidget/BaseFeatureDetail.tsx 44.97% <18.01%> (-24.38%) ⬇️
packages/core/util/index.ts 81.81% <78.57%> (-0.61%) ⬇️
... and 2 more

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@cmdcolin cmdcolin force-pushed the sequence_dialog branch 2 times, most recently from 987aa24 to 6c24098 Compare March 4, 2021 11:23
@rbuels rbuels merged commit 08aeb46 into master Mar 4, 2021
@rbuels rbuels deleted the sequence_dialog branch March 4, 2021 22:10
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2 participants