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Added a slightly more helpful error message to the reads filter

Open jamesemery opened this issue 2 years ago • 3 comments

Fixes #7944

jamesemery avatar Jul 15 '22 20:07 jamesemery

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

gatk-bot avatar Jul 15 '22 20:07 gatk-bot

Codecov Report

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

:exclamation: 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%) :arrow_down:
...broadinstitute/hellbender/utils/svd/SimpleSVD.java 0.000% <0.000%> (-100.000%) :arrow_down:
...titute/hellbender/utils/UnvalidatingGenomeLoc.java 0.000% <0.000%> (-100.000%) :arrow_down:
...itute/hellbender/utils/locusiterator/LIBSTest.java 0.000% <0.000%> (-100.000%) :arrow_down:
...ute/hellbender/tools/htsgetreader/HtsgetClass.java 0.000% <0.000%> (-100.000%) :arrow_down:
...te/hellbender/tools/htsgetreader/HtsgetFormat.java 0.000% <0.000%> (-100.000%) :arrow_down:
...ender/utils/svd/ApacheSingularValueDecomposer.java 0.000% <0.000%> (-100.000%) :arrow_down:
...ender/utils/svd/OjAlgoSingularValueDecomposer.java 0.000% <0.000%> (-100.000%) :arrow_down:
...nder/utils/downsampling/FractionalDownsampler.java 0.000% <0.000%> (-100.000%) :arrow_down:
...der/cmdline/programgroups/ExampleProgramGroup.java 0.000% <0.000%> (-100.000%) :arrow_down:
... and 1144 more

codecov[bot] avatar Jul 15 '22 21:07 codecov[bot]

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

jamesemery avatar Jul 19 '22 14:07 jamesemery