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magicDGS / ReadTools

A Universal Toolkit for Handling Sequence Data from Different Sequencing Platforms
https://magicdgs.github.io/ReadTools/
MIT License
6 stars 3 forks source link

Support java.nio.Path with FASTQ input files #473

Closed magicDGS closed 6 years ago

magicDGS commented 6 years ago

Previously our ReadReaderFactory was calling Path.toFile for FASTQ input, which might file for non-local files. This commit fix this bug and also removes non-Path methods in ReadReaderFactory for simplify codepaths.

Fixes #472

codecov[bot] commented 6 years ago

Codecov Report

Merging #473 into master will increase coverage by 0.03%. The diff coverage is 100%.

Impacted file tree graph

@@              Coverage Diff               @@
##              master      #473      +/-   ##
==============================================
+ Coverage     93.386%   93.417%   +0.03%     
+ Complexity       993       991       -2     
==============================================
  Files             95        95              
  Lines           2646      2643       -3     
  Branches         284       284              
==============================================
- Hits            2471      2469       -2     
+ Misses           134       133       -1     
  Partials          41        41
Impacted Files Coverage Δ Complexity Δ
...gicdgs/readtools/utils/read/ReadReaderFactory.java 80% <100%> (+2.222%) 6 <1> (-2) :arrow_down: