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Created "variantcalling" test group and split them off from the rest of the integration tests for runtime purposes #4984

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merged 3 commits into from
Jul 6, 2018

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Fixes #4983

@jamesemery jamesemery requested a review from droazen July 5, 2018 16:44
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codecov-io commented Jul 5, 2018

Codecov Report

Merging #4984 into master will decrease coverage by 0.014%.
The diff coverage is n/a.

@@               Coverage Diff               @@
##              master     #4984       +/-   ##
===============================================
- Coverage     80.787%   80.773%   -0.014%     
+ Complexity     17966     17950       -16     
===============================================
  Files           1095      1095               
  Lines          64619     64619               
  Branches       10400     10400               
===============================================
- Hits           52204     52195        -9     
- Misses          8389      8395        +6     
- Partials        4026      4029        +3
Impacted Files Coverage Δ Complexity Δ
...oadinstitute/hellbender/utils/pairhmm/PairHMM.java 74.286% <0%> (-3.571%) 24% <0%> (ø)
...hellbender/utils/pairhmm/VectorLoglessPairHMM.java 82.895% <0%> (-1.316%) 11% <0%> (ø)
...e/hellbender/engine/AbstractConcordanceWalker.java 87.952% <0%> (-1.205%) 13% <0%> (-1%)
...rs/annotator/allelespecific/AS_StrandBiasTest.java 85.366% <0%> (-0.813%) 43% <0%> (-1%)
...kers/variantutils/PosteriorProbabilitiesUtils.java 81.41% <0%> (-0.641%) 50% <0%> (-8%)

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One comment to address, then this is good to merge 👍

build.gradle Outdated
} else if (TEST_TYPE == "python") {
includeGroups "python"
} else if (TEST_TYPE == "all"){
//include everything
} else {
excludeGroups "cloud", "bucket", "python", "funcotatorValidation"
excludeGroups "cloud", "bucket", "python", "funcotatorValidation", "variantcalling"
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I think that the variantcalling tests should not be excluded in the else clause here, since the intention of the else clause is to include all the "normal" (unit/integration) tests, I believe.

@jamesemery jamesemery merged commit cee1d46 into master Jul 6, 2018
@davidbenjamin davidbenjamin deleted the je_splitIntegrationTests branch February 24, 2021 15:06
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3 participants