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epam / fonda

Fonda is a framework which offers scalable and automatic analysis of multiple NGS sequencing data types
Apache License 2.0
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issue #196: Fix @RG tag in sam/bam file output #200

Open kamyshova opened 3 years ago

kamyshova commented 3 years ago

Resolves #196 The pull request provides @RG ID tag building - add lane to sample name if exists and get the LB tag for all workflows.

codecov-commenter commented 3 years ago

Codecov Report

Merging #200 (80b56aa) into develop (89571ad) will decrease coverage by 0.01%. The diff coverage is 85.71%.

:exclamation: Current head 80b56aa differs from pull request most recent head a6167cc. Consider uploading reports for the commit a6167cc to get more accurate results Impacted file tree graph

@@              Coverage Diff              @@
##             develop     #200      +/-   ##
=============================================
- Coverage      89.74%   89.73%   -0.02%     
+ Complexity       648      645       -3     
=============================================
  Files            118      118              
  Lines           3482     3477       -5     
  Branches         214      211       -3     
=============================================
- Hits            3125     3120       -5     
  Misses           255      255              
  Partials         102      102
Impacted Files Coverage Δ Complexity Δ
...c/main/java/com/epam/fonda/tools/impl/BwaSort.java 94.73% <83.33%> (-0.51%) 3.00 <0.00> (-2.00)
.../java/com/epam/fonda/tools/impl/NovoalignSort.java 91.11% <83.33%> (-0.56%) 5.00 <0.00> (-2.00)
src/main/java/com/epam/fonda/utils/DnaUtils.java 98.48% <100.00%> (+0.04%) 17.00 <1.00> (+1.00)

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