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add error message for when tree-score-threshold is set in ReblockGVCF… #8218

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merged 2 commits into from
Feb 23, 2023

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meganshand
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…s without TREE_SCORE present

Addresses #8203

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gatk-bot commented Feb 22, 2023

Github actions tests reported job failures from actions build 4244812025
Failures in the following jobs:

Test Type JDK Job ID Logs
integration 11.0.11+9 4244812025.12 logs
integration 8 4244812025.0 logs

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codecov bot commented Feb 22, 2023

Codecov Report

Merging #8218 (fbdeba4) into master (b7f24ff) will increase coverage by 0.004%.
The diff coverage is 100.000%.

Additional details and impacted files
@@               Coverage Diff               @@
##              master     #8218       +/-   ##
===============================================
+ Coverage     86.652%   86.655%   +0.004%     
- Complexity     39151     39169       +18     
===============================================
  Files           2346      2346               
  Lines         183621    183670       +49     
  Branches       20148     20152        +4     
===============================================
+ Hits          159111    159160       +49     
- Misses         17447     17450        +3     
+ Partials        7063      7060        -3     
Impacted Files Coverage Δ
...bender/tools/walkers/variantutils/ReblockGVCF.java 80.340% <100.000%> (+0.096%) ⬆️
...lkers/variantutils/ReblockGVCFIntegrationTest.java 98.052% <100.000%> (+0.059%) ⬆️
...ls/walkers/qc/TransferReadTagsIntegrationTest.java 94.118% <0.000%> (-1.882%) ⬇️
...der/tools/walkers/variantutils/SelectVariants.java 83.619% <0.000%> (-0.292%) ⬇️
...institute/hellbender/utils/read/FlowBasedRead.java 53.600% <0.000%> (-0.093%) ⬇️
...org/broadinstitute/hellbender/engine/GATKTool.java 90.083% <0.000%> (ø)
...itute/hellbender/tools/LocalAssemblerUnitTest.java 92.448% <0.000%> (ø)
...nder/engine/filters/VariantTypesVariantFilter.java 100.000% <0.000%> (ø)
...rs/variantutils/SelectVariantsIntegrationTest.java 96.959% <0.000%> (+0.031%) ⬆️
...e/hellbender/utils/read/FlowBasedReadUnitTest.java 95.402% <0.000%> (+0.108%) ⬆️
... and 3 more

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This looks good... i'm a little worried as to why the tool is partiularly slow when the annotation isn't present but this seems like a good

@meganshand meganshand merged commit 24f62de into master Feb 23, 2023
@meganshand meganshand deleted the ms_tree_check branch February 23, 2023 17:37
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3 participants