Read Orientation Model test case where the variant is no longer emitted in the vcf

[takutosato]

One of the variants is no longer emitted in vcf, potentially due to #5078. Somehow this was not caught by the remote test for #4895.

[takutosato]

@cmnbroad will you review?

[cmnbroad]

Since this branch passed before it was merged, it does seem likely that the failure is the result of some interaction with #5078 - would suggest making a ticket to track down the root cause. Otherwise looks good. We can merge when tests pass.

[codecov-io]

Codecov Report

Merging #5091 into master will increase coverage by 13.344%.
The diff coverage is n/a.

@@               Coverage Diff                @@
##              master     #5091        +/-   ##
================================================
+ Coverage     73.139%   86.483%   +13.344%     
- Complexity     24660     29154      +4494     
================================================
  Files           1813      1813                
  Lines         135228    135227         -1     
  Branches       15020     15020                
================================================
+ Hits           98905    116949     +18044     
+ Misses         31562     12818     -18744     
- Partials        4761      5460       +699

Impacted Files	Coverage Δ	Complexity Δ
...ientation/ReadOrientationModelIntegrationTest.java	100% <ø> (+98.361%)	6 <0> (+5)	⬆️
.../markduplicates/MarkDuplicatesScoringStrategy.java	82.353% <0%> (ø)	7% <0%> (+1%)	⬆️
...nstitute/hellbender/utils/read/AlignmentUtils.java	75.605% <0%> (+0.202%)	149% <0%> (+1%)	⬆️
...k/sv/discovery/inference/BreakpointsInference.java	76.471% <0%> (+0.392%)	14% <0%> (ø)	⬇️
...lbender/utils/read/SAMRecordToGATKReadAdapter.java	92.126% <0%> (+0.394%)	136% <0%> (+1%)	⬆️
...otator/dataSources/gencode/GencodeFuncotation.java	61.726% <0%> (+0.442%)	219% <0%> (+1%)	⬆️
...stitute/hellbender/utils/clipping/ReadClipper.java	69.945% <0%> (+0.546%)	74% <0%> (+2%)	⬆️
...lkers/annotator/allelespecific/AS_RankSumTest.java	82.822% <0%> (+0.614%)	48% <0%> (ø)	⬇️
...oadinstitute/hellbender/utils/gcs/BucketUtils.java	80% <0%> (+0.645%)	40% <0%> (ø)	⬇️
...broadinstitute/hellbender/utils/IntervalUtils.java	91.516% <0%> (+0.722%)	181% <0%> (ø)	⬇️
... and 535 more