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Mark --disable-tool-default-read-filters as advanced, and add a warning to its documentation string #4671

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droazen
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@droazen droazen commented Apr 18, 2018

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droazen commented Apr 18, 2018

@cmnbroad please review

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👍 when tests pass.

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Codecov Report

Merging #4671 into master will decrease coverage by 0.005%.
The diff coverage is 100%.

@@              Coverage Diff               @@
##             master     #4671       +/-   ##
==============================================
- Coverage     79.84%   79.835%   -0.005%     
+ Complexity    17330     17328        -2     
==============================================
  Files          1074      1074               
  Lines         62907     62907               
  Branches      10181     10181               
==============================================
- Hits          50225     50222        -3     
- Misses         8701      8704        +3     
  Partials       3981      3981
Impacted Files Coverage Δ Complexity Δ
...lugin/DefaultGATKReadFilterArgumentCollection.java 100% <100%> (ø) 4 <0> (ø) ⬇️
...utils/smithwaterman/SmithWatermanIntelAligner.java 50% <0%> (-30%) 1% <0%> (-2%)

@droazen droazen merged commit a5386fd into master Apr 18, 2018
@droazen droazen deleted the dr_mark_disable_tool_default_read_filters_as_advanced branch April 18, 2018 15:54
cwhelan pushed a commit to cwhelan/gatk-linked-reads that referenced this pull request May 25, 2018
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3 participants