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Allow opening plaintext .vcf files from the "Add track" workflow #2126

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merged 2 commits into from
Jul 15, 2021

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This adds the VcfAdapter for a plain VCF to both CLI and add-track. It doesn't really try to warn against large VCFs but it should be fine for small VCF that are encountered in the wild. The VcfAdapter was created by @carolinebridge-oicr originally

We could think about also unifying the cli and core codebase, and making it more pluggable perhaps too...but maybe as follow ons :)

Update cli guessAdapter
@github-actions github-actions bot added the needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) label Jul 13, 2021
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codecov bot commented Jul 13, 2021

Codecov Report

Merging #2126 (5589107) into main (ec358f4) will decrease coverage by 0.02%.
The diff coverage is n/a.

❗ Current head 5589107 differs from pull request most recent head 98bb881. Consider uploading reports for the commit 98bb881 to get more accurate results
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@@            Coverage Diff             @@
##             main    #2126      +/-   ##
==========================================
- Coverage   61.99%   61.96%   -0.03%     
==========================================
  Files         476      476              
  Lines       22781    22781              
  Branches     5351     5351              
==========================================
- Hits        14123    14117       -6     
- Misses       8377     8383       +6     
  Partials      281      281              
Impacted Files Coverage Δ
packages/core/util/tracks.ts 64.86% <ø> (ø)
products/jbrowse-cli/src/commands/add-track.ts 53.27% <ø> (ø)
...nts/src/SNPCoverageRenderer/SNPCoverageRenderer.ts 80.24% <0.00%> (-7.41%) ⬇️

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@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 Jul 13, 2021
@cmdcolin cmdcolin changed the title Add plain vcf adapter recognition to guessAdapter Add plain VCF adapter recognition to guessAdapter Jul 13, 2021
@cmdcolin cmdcolin merged commit b051812 into main Jul 15, 2021
@cmdcolin cmdcolin deleted the add_plain_vcf_adapter branch July 15, 2021 17:21
@cmdcolin cmdcolin changed the title Add plain VCF adapter recognition to guessAdapter Allow opening plaintext .vcf files from the "Add track" workflow Jul 26, 2021
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