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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

Upgrade to GATK 4.0.2.1-ReadTools and HTSJDK 1.14.3 #442

Closed magicDGS closed 6 years ago

magicDGS commented 6 years ago

Finishes (mostly) https://github.com/magicDGS/ReadTools/projects/9

Closes #180 Closes #370 Closes #372

magicDGS commented 6 years ago

Should check if every issue in the project is solved by this.

codecov[bot] commented 6 years ago

Codecov Report

Merging #442 into master will decrease coverage by 0.485%. The diff coverage is 59.375%.

Impacted file tree graph

@@              Coverage Diff               @@
##              master     #442       +/-   ##
==============================================
- Coverage     93.715%   93.23%   -0.485%     
+ Complexity       834      833        -1     
==============================================
  Files             81       81               
  Lines           2307     2319       +12     
  Branches         250      254        +4     
==============================================
  Hits            2162     2162               
- Misses           109      120       +11     
- Partials          36       37        +1
Impacted Files Coverage Δ Complexity Δ
...adtools/tools/quality/QualityEncodingDetector.java 71.429% <ø> (ø) 4 <0> (ø) :arrow_down:
src/main/java/org/magicdgs/readtools/Main.java 84.375% <ø> (ø) 14 <0> (ø) :arrow_down:
...n/java/org/magicdgs/readtools/RTHelpConstants.java 100% <100%> (ø) 3 <0> (ø) :arrow_down:
...eadtools/utils/trimming/TrimAndFilterPipeline.java 100% <100%> (ø) 15 <3> (-2) :arrow_down:
...rg/magicdgs/readtools/engine/ReadToolsProgram.java 72.727% <30.769%> (-17.595%) 12 <1> (+1)
.../readtools/cmd/plugin/TrimmerPluginDescriptor.java 90.84% <63.636%> (-2.017%) 52 <5> (ø)