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Add BEDPE adapter type #3341

Merged
merged 1 commit into from
Nov 23, 2022
Merged

Add BEDPE adapter type #3341

merged 1 commit into from
Nov 23, 2022

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cmdcolin
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@cmdcolin cmdcolin commented Nov 18, 2022

Fixes #306

This adds an adapter type for BEDPE files. It creates two SimpleFeature objects for each line of the BED file

  1. SimpleFeature with col 1-3 as the primary "location" with a mate field containing columns 4-6
  2. SimpleFeature with col 4-6 as the primary "location" with a mate field containing columns 1-3

in this way, these two features "reciprocally point at each other" a little like BND in a VCF file

this is just an initial concept, would be nice to have "arc view" of these features and "breakpoint split view" type stuff, but may need to check support for this

@github-actions github-actions bot added the needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) label Nov 18, 2022
@cmdcolin
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(just for initial assesment the arc display would not work with feature+mate like this, it connects a feature start and end)

@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 Nov 18, 2022
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codecov bot commented Nov 23, 2022

Codecov Report

Merging #3341 (f15af13) into main (a0df793) will decrease coverage by 0.21%.
The diff coverage is 18.62%.

@@            Coverage Diff             @@
##             main    #3341      +/-   ##
==========================================
- Coverage   59.17%   58.96%   -0.22%     
==========================================
  Files         751      757       +6     
  Lines       29277    29413     +136     
  Branches     7085     7116      +31     
==========================================
+ Hits        17325    17342      +17     
- Misses      11758    11877     +119     
  Partials      194      194              
Impacted Files Coverage Δ
plugins/bed/src/BedpeAdapter/BedpeAdapter.ts 0.00% <0.00%> (ø)
plugins/bed/src/BedpeAdapter/configSchema.ts 50.00% <50.00%> (ø)
plugins/bed/src/BedAdapter/index.ts 75.00% <75.00%> (ø)
plugins/bed/src/BedTabixAdapter/index.ts 75.00% <75.00%> (ø)
plugins/bed/src/BedpeAdapter/index.ts 75.00% <75.00%> (ø)
plugins/bed/src/index.ts 88.23% <92.85%> (+3.45%) ⬆️
plugins/bed/src/BigBedAdapter/index.ts 100.00% <100.00%> (ø)
plugins/hic/src/HicRenderer/HicRenderer.tsx 95.45% <0.00%> (-4.55%) ⬇️
plugins/alignments/src/BamAdapter/BamAdapter.ts 70.79% <0.00%> (-0.89%) ⬇️

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@cmdcolin cmdcolin marked this pull request as ready for review November 23, 2022 13:41
@cmdcolin cmdcolin merged commit f664275 into main Nov 23, 2022
@cmdcolin cmdcolin deleted the bedpe_adapter branch November 23, 2022 16:18
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Create BEDPE parser
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