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Test start equals end in tabix, and make sure end overlaps work #94

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merged 2 commits into from
Apr 6, 2020

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cmdcolin
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@cmdcolin cmdcolin commented Apr 6, 2020

This tests a special situation of a VCF where the start and end parameters are set to be the same e.g.

tabix -0 -s 1 -b 2 -e 2 -f out.bed.gz

A file is attached as a test

This is assumed to be a 1bp wide feature.

It also adds some more curlies because it looks better to me :)

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codecov bot commented Apr 6, 2020

Codecov Report

Merging #94 into master will increase coverage by 0.08%.
The diff coverage is 89.47%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #94      +/-   ##
==========================================
+ Coverage   90.71%   90.79%   +0.08%     
==========================================
  Files           7        7              
  Lines         549      554       +5     
  Branches      150      150              
==========================================
+ Hits          498      503       +5     
  Misses         51       51              
Impacted Files Coverage Δ
src/tabixIndexedFile.ts 91.62% <89.47%> (+0.24%) ⬆️

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@cmdcolin cmdcolin merged commit c3fe695 into master Apr 6, 2020
@garrettjstevens
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This tests a special situation of a VCF where...

Did you mean BED instead of VCF (since that's what the test file is)?

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cmdcolin commented Apr 6, 2020

Ya it was a BED file not a VCF..mistyped

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cmdcolin commented Apr 6, 2020

And, strictly speaking, it was not a BED file, it is a custom file where you just have a refName:position, in what I think implies 1bp wide feature, so I implemented it this way

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Got it, makes sense

@rbuels rbuels deleted the test_start_end branch April 6, 2020 18:51
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2 participants