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Added a slightly more helpful error message to the reads filter #7947

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merged 2 commits into from
Dec 23, 2022

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jamesemery
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Fixes #7944

@jamesemery jamesemery requested a review from droazen July 15, 2022 20:13
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gatk-bot commented Jul 15, 2022

Github actions tests reported job failures from actions build 2679127706
Failures in the following jobs:

Test Type JDK Job ID Logs
unit 11 2679127706.13 logs
unit 8 2679127706.1 logs

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codecov bot commented Jul 15, 2022

Codecov Report

Merging #7947 (413983a) into master (e81a361) will decrease coverage by 40.864%.
The diff coverage is 100.000%.

❗ Current head 413983a differs from pull request most recent head 7791882. Consider uploading reports for the commit 7791882 to get more accurate results

@@               Coverage Diff                @@
##              master     #7947        +/-   ##
================================================
- Coverage     86.981%   46.116%   -40.864%     
+ Complexity     36962     24011     -12951     
================================================
  Files           2221      2217         -4     
  Lines         173894    173851        -43     
  Branches       18785     18792         +7     
================================================
- Hits          151254     80174     -71080     
- Misses         15998     87790     +71792     
+ Partials        6642      5887       -755     
Impacted Files Coverage Δ
.../hellbender/engine/filters/CountingReadFilter.java 60.215% <100.000%> (-39.785%) ⬇️
...broadinstitute/hellbender/utils/svd/SimpleSVD.java 0.000% <0.000%> (-100.000%) ⬇️
...titute/hellbender/utils/UnvalidatingGenomeLoc.java 0.000% <0.000%> (-100.000%) ⬇️
...itute/hellbender/utils/locusiterator/LIBSTest.java 0.000% <0.000%> (-100.000%) ⬇️
...ute/hellbender/tools/htsgetreader/HtsgetClass.java 0.000% <0.000%> (-100.000%) ⬇️
...te/hellbender/tools/htsgetreader/HtsgetFormat.java 0.000% <0.000%> (-100.000%) ⬇️
...ender/utils/svd/ApacheSingularValueDecomposer.java 0.000% <0.000%> (-100.000%) ⬇️
...ender/utils/svd/OjAlgoSingularValueDecomposer.java 0.000% <0.000%> (-100.000%) ⬇️
...nder/utils/downsampling/FractionalDownsampler.java 0.000% <0.000%> (-100.000%) ⬇️
...der/cmdline/programgroups/ExampleProgramGroup.java 0.000% <0.000%> (-100.000%) ⬇️
... and 1144 more

@jamesemery
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@droazen I fixed the tests. Can you take a look? I know you have opinions

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@lbergelson lbergelson left a comment

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@jamesemery 👍 good idea.

@lbergelson lbergelson merged commit 640d921 into master Dec 23, 2022
@lbergelson lbergelson deleted the je_totalReadsInFilterMessage branch December 23, 2022 20:51
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The HaplotypeCaller read filter status indicator should include the number of un-filtered reads for comparison
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