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Add non-indexed and plaintext VCF Adapter to variants plugin #2068

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merged 13 commits into from
Jun 30, 2021

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carolinebridge
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solves this issue for jbrowse-plugin-gdc while providing the functionality to core

@carolinebridge carolinebridge requested a review from cmdcolin June 23, 2021 14:34
@carolinebridge carolinebridge self-assigned this Jun 23, 2021
@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 23, 2021
@carolinebridge carolinebridge added the enhancement New feature or request label Jun 23, 2021
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codecov bot commented Jun 23, 2021

Codecov Report

Merging #2068 (768b119) into main (d18857c) will increase coverage by 0.03%.
The diff coverage is 87.27%.

Impacted file tree graph

@@            Coverage Diff             @@
##             main    #2068      +/-   ##
==========================================
+ Coverage   61.41%   61.44%   +0.03%     
==========================================
  Files         479      480       +1     
  Lines       22908    22963      +55     
  Branches     5249     5264      +15     
==========================================
+ Hits        14068    14110      +42     
- Misses       8565     8578      +13     
  Partials      275      275              
Impacted Files Coverage Δ
packages/core/util/tracks.ts 64.86% <ø> (ø)
plugins/variants/src/index.ts 95.23% <66.66%> (-4.77%) ⬇️
plugins/variants/src/VcfAdapter/VcfAdapter.ts 88.46% <88.46%> (ø)
...nts/src/SNPCoverageRenderer/SNPCoverageRenderer.ts 80.24% <0.00%> (-7.41%) ⬇️

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@cmdcolin
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could this code work if it was a plain text vcf? could possible check if there is the magic number in the buffer https://en.wikipedia.org/wiki/Gzip e.g. 1f8b and only unzip buffer in that case

@cmdcolin
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Can you update the PR title to be a "sentence style" title? We try to make them sort of like this cause they appear directly in our changelog (e.g. https://jbrowse.org/jb2/blog/2021/05/24/v1.3.0-release#130-2021-05-24)

@carolinebridge carolinebridge changed the title [template_for_vcfadapter] implements non-indexed vcf adapter Add non-indexed and plaintext VCF Adapter to variants plugin Jun 25, 2021
@carolinebridge carolinebridge removed the needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) label Jun 25, 2021
@carolinebridge carolinebridge requested a review from cmdcolin June 25, 2021 20:04
@cmdcolin cmdcolin force-pushed the template_for_vcfadapter branch from d19c34f to 768b119 Compare June 29, 2021 14:54
@cmdcolin cmdcolin merged commit 45e5806 into main Jun 30, 2021
@cmdcolin cmdcolin deleted the template_for_vcfadapter branch June 30, 2021 17:54
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2 participants