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timbitz / Whippet.jl

Lightweight and Fast; RNA-seq quantification at the event-level
MIT License
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Increase buffer sizes for input files #82

Closed timbitz closed 5 years ago

timbitz commented 5 years ago

This is a temporary fix for buggy empty line behavior of readline function in BufferedStreams.jl v0.4.1 which caused whippet-delta.jl to prematurely terminate when comparing only two samples (though multi-sample comparisons still works as expected).

This PR increases buffer size beyond expected .psi.gz filesize as a solution and adds additional assertion sanity checks. Note: This bug is already fixed in BufferedStreams.jl v1.0.0, so once the Whippet v1.0.0 update is ready this will be a non-issue.

codecov[bot] commented 5 years ago

Codecov Report

Merging #82 into master will decrease coverage by 0.05%. The diff coverage is 0%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #82      +/-   ##
==========================================
- Coverage   58.99%   58.94%   -0.05%     
==========================================
  Files          19       19              
  Lines        2370     2372       +2     
==========================================
  Hits         1398     1398              
- Misses        972      974       +2
Impacted Files Coverage Δ
src/diff.jl 0% <0%> (ø) :arrow_up:

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