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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

Add stacktrace always to unexpected errors #517

Closed magicDGS closed 5 years ago

magicDGS commented 5 years ago

This commit prints always the stacktrace for unexpected errors, because their messages usually are not useful for the user but can help debugging without re-running with --verbosity DEBUG

In addition this commit removes the PrintStream fields in Main, which were only visible for testing - now there are methods in the test base class to capture stderr/stdout in an easier manner.

Closes https://github.com/magicDGS/ReadTools/issues/514

codecov[bot] commented 5 years ago

Codecov Report

Merging #517 into master will decrease coverage by 0.007%. The diff coverage is 100%.

Impacted file tree graph

@@              Coverage Diff               @@
##              master     #517       +/-   ##
==============================================
- Coverage     93.556%   93.55%   -0.007%     
  Complexity      1077     1077               
==============================================
  Files            103      103               
  Lines           2840     2837        -3     
  Branches         302      302               
==============================================
- Hits            2657     2654        -3     
  Misses           137      137               
  Partials          46       46
Impacted Files Coverage Δ Complexity Δ
src/main/java/org/magicdgs/readtools/Main.java 83.333% <100%> (-1.515%) 15 <2> (ø)