Fix for gatk-5449

[kgururaj]

CI test

[codecov-io]

Codecov Report

Merging #5799 into master will decrease coverage by 2.577%.
The diff coverage is 0%.

@@               Coverage Diff               @@
##              master     #5799       +/-   ##
===============================================
- Coverage     87.041%   84.463%   -2.577%     
+ Complexity     32076     31118      -958     
===============================================
  Files           1977      1977               
  Lines         147082    147085        +3     
  Branches       16171     16171               
===============================================
- Hits          128021    124233     -3788     
- Misses         13157     16917     +3760     
- Partials        5904      5935       +31

Impacted Files	Coverage Δ	Complexity Δ
...ls/genomicsdb/GenomicsDBImportIntegrationTest.java	9.251% <0%> (-79.219%)	2 <0> (-78)
...s/GermlineContigPloidyModelArgumentCollection.java	0% <0%> (-100%)	0% <0%> (-4%)
...mlineContigPloidyHybridADVIArgumentCollection.java	0% <0%> (-100%)	0% <0%> (-3%)
...ments/GermlineCNVHybridADVIArgumentCollection.java	0% <0%> (-100%)	0% <0%> (-3%)
...r/arguments/GermlineCallingArgumentCollection.java	0% <0%> (-100%)	0% <0%> (-4%)
...ect/filtering/ChimericOriginalAlignmentFilter.java	0% <0%> (-100%)	0% <0%> (-8%)
...tools/examples/ExampleStreamingPythonExecutor.java	0% <0%> (-96.667%)	0% <0%> (-8%)
...ents/GermlineDenoisingModelArgumentCollection.java	0% <0%> (-96.552%)	0% <0%> (-4%)
...number/arguments/HybridADVIArgumentCollection.java	0% <0%> (-94.915%)	0% <0%> (-3%)
...ct/CreateSomaticPanelOfNormalsIntegrationTest.java	3.448% <0%> (-94.253%)	2% <0%> (-8%)
... and 111 more

[ldgauthier]

I didn't confirm that the test fails without the fix, but that test replicates my issue.

[droazen]

@kgururaj If you can resolve the remaining conflict, we can get this one merged now that tests are passing.

[kgururaj]

Done

[droazen]

👍