Spark 3.3.0 - WIP.

[cmnbroad]

No description provided.

[gatk-bot]

Github actions tests reported job failures from actions build 2578792940
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
cloud	17	2578792940.11	logs
unit	17	2578792940.13	logs
integration	17	2578792940.12	logs

[gatk-bot]

Github actions tests reported job failures from actions build 2624287216
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	17	2624287216.13	logs
cloud	17	2624287216.11	logs
integration	17	2624287216.12	logs

[gatk-bot]

Github actions tests reported job failures from actions build 2624794723
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	17	2624794723.13	logs
cloud	17	2624794723.11	logs
integration	17	2624794723.12	logs

[gatk-bot]

Github actions tests reported job failures from actions build 2625798157
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	17	2625798157.13	logs
cloud	17	2625798157.11	logs

[gatk-bot]

Github actions tests reported job failures from actions build 2625894786
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
cloud	17	2625894786.11	logs
unit	17	2625894786.13	logs
integration	17	2625894786.12	logs

[gatk-bot]

Github actions tests reported job failures from actions build 2632297364
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
cloud	17	2632297364.11	logs
unit	17	2632297364.13	logs
integration	17	2632297364.12	logs

[gatk-bot]

Github actions tests reported job failures from actions build 2650555864
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	17	2650555864.13	logs
cloud	17	2650555864.11	logs
integration	17	2650555864.12	logs

[gatk-bot]

Github actions tests reported job failures from actions build 2651387279
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
cloud	17	2651387279.11	logs
unit	17	2651387279.13	logs

[gatk-bot]

Github actions tests reported job failures from actions build 2651609966
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	17	2651609966.13	logs
cloud	17	2651609966.11	logs
integration	17	2651609966.12	logs

[gatk-bot]

Github actions tests reported job failures from actions build 2652121060
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	17	2652121060.13	logs
integration	17	2652121060.12	logs

[gatk-bot]

Github actions tests reported job failures from actions build 2966654286
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	17	2966654286.1	logs
conda	17	2966654286.3	logs
integration	17	2966654286.0	logs
variantcalling	17	2966654286.2	logs

[gatk-bot]

Github actions tests reported job failures from actions build 2968128596
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	17	2968128596.1	logs
conda	17	2968128596.3	logs
integration	17	2968128596.0	logs
variantcalling	17	2968128596.2	logs

[gatk-bot]

Github actions tests reported job failures from actions build 2972474666
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	17	2972474666.1	logs
variantcalling	17	2972474666.2	logs
conda	17	2972474666.3	logs
integration	17	2972474666.0	logs

[gatk-bot]

Github actions tests reported job failures from actions build 2973021281
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	17	2973021281.1	logs
integration	17	2973021281.0	logs
variantcalling	17	2973021281.2	logs
conda	17	2973021281.3	logs

[gatk-bot]

Github actions tests reported job failures from actions build 2973346685
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	17	2973346685.1	logs
conda	17	2973346685.3	logs
integration	17	2973346685.0	logs
variantcalling	17	2973346685.2	logs

[gatk-bot]

Github actions tests reported job failures from actions build 2974297830
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	17	2974297830.1	logs
integration	17	2974297830.0	logs
variantcalling	17	2974297830.2	logs

[gatk-bot]

Github actions tests reported job failures from actions build 2974887773
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	17	2974887773.1	logs
variantcalling	17	2974887773.2	logs
integration	17	2974887773.0	logs

[gatk-bot]

Github actions tests reported job failures from actions build 2979443533
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	17	2979443533.1	logs
variantcalling	17	2979443533.2	logs
integration	17	2979443533.0	logs

[gatk-bot]

Github actions tests reported job failures from actions build 2980069635
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	17	2980069635.1	logs
variantcalling	17	2980069635.2	logs
integration	17	2980069635.0	logs

[codecov]

Codecov Report

Merging #7920 (d5cf9d7) into master (993c7f1) will decrease coverage by 42.390%.
The diff coverage is 72.727%.

❗ Current head d5cf9d7 differs from pull request most recent head cb66210. Consider uploading reports for the commit cb66210 to get more accurate results

Additional details and impacted files

@@               Coverage Diff                @@
##              master     #7920        +/-   ##
================================================
- Coverage     86.663%   44.273%   -42.390%     
+ Complexity     38829     25594     -13235     
================================================
  Files           2331      2208       -123     
  Lines         182003    173556      -8447     
  Branches       19985     18708      -1277     
================================================
- Hits          157729     76838     -80891     
- Misses         17262     91256     +73994     
+ Partials        7012      5462      -1550     

Impacted Files	Coverage Δ
...ellbender/tools/dragstr/CalibrateDragstrModel.java	70.345% <ø> (ø)
...r/utils/fasta/CachingIndexedFastaSequenceFile.java	70.330% <ø> (-1.099%)	⬇️
...t/java/org/broadinstitute/hellbender/MainTest.java	2.564% <ø> (-82.182%)	⬇️
...Plugin/GATKAnnotationPluginDescriptorUnitTest.java	7.219% <ø> (-81.016%)	⬇️
...GATKPlugin/GATKReadFilterPluginDescriptorTest.java	0.484% <ø> (-88.136%)	⬇️
...lbender/engine/AssemblyRegionIteratorUnitTest.java	1.639% <0.000%> (-80.328%)	⬇️
...gine/spark/datasources/ReadsSparkSinkUnitTest.java	1.538% <ø> (-74.615%)	⬇️
...e/spark/datasources/VariantsSparkSinkUnitTest.java	1.481% <ø> (-82.963%)	⬇️
...bender/tools/spark/PileupSparkIntegrationTest.java	2.041% <ø> (-95.959%)	⬇️
...der/tools/walkers/sv/SVClusterIntegrationTest.java	0.504% <0.000%> (-98.992%)	⬇️
... and 1046 more

[cmnbroad]

Closing in favor of #8035.