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Add support for breakends in VCF #163

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merged 4 commits into from May 22, 2019
Merged

Add support for breakends in VCF #163

merged 4 commits into from May 22, 2019

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alumi
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@alumi alumi commented May 17, 2019

Summary

This PR adds basic support for breakends in VCF.
Breakends are variant records which have SVTYPE=BND in the INFO field.
They have a dedicated format of string representation for ALT field.
For more details, please refer to the spec "5.4 Specifying complex rearrangements with breakends"

Tests

  • lein check 馃啑
  • lein test :all 馃啑
  • lein cloverage 馃啑

@alumi alumi requested review from athos and r6eve May 17, 2019 08:09
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codecov bot commented May 17, 2019

Codecov Report

Merging #163 into master will increase coverage by 0.08%.
The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff            @@
##           master    #163      +/-   ##
=========================================
+ Coverage   86.02%   86.1%   +0.08%     
=========================================
  Files          71      71              
  Lines        5387    5419      +32     
  Branches      489     489              
=========================================
+ Hits         4634    4666      +32     
  Misses        264     264              
  Partials      489     489
Impacted Files Coverage 螖
src/cljam/io/vcf/util.clj 90.52% <100%> (+1.91%) 猬嗭笍

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@alumi
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alumi commented May 20, 2019

Resolved conflicts with #162

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@r6eve r6eve left a comment

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Thank you for the breakends support.
I'm halfway through my review. I left a comment about regexp.

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Thank you for working on this improvement 馃憤 Basically, it looks good to me.
Added a couple of minor comments.

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LGTM!

@r6eve r6eve merged commit 7b5d627 into master May 22, 2019
@r6eve r6eve deleted the feature/breakends branch May 22, 2019 08:50
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alumi commented May 22, 2019

Thanks!! 馃帀

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3 participants