Adding argument to GenotypeGVCFs to keep only RAW_GT_COUNT

[meganshand]

Currently, there is an argument to keep all raw annotations, but the flow based pipeline has a use case that needs to keep RAW_GT_COUNT without keeping the other raw annotations. This new argument allows the user to keep RAW_GT_COUNT while still cleaning up the other raw annotations in GenotypeGVCFs.

[codecov[bot]]

Codecov Report

Merging #7996 (f7b8aa9) into master (05a7634) will increase coverage by 7.336%. The diff coverage is 89.796%.

Additional details and impacted files

@@               Coverage Diff               @@
##              master     #7996       +/-   ##
===============================================
+ Coverage     79.301%   86.637%   +7.336%     
- Complexity     36613     38937     +2324     
===============================================
  Files           2328      2335        +7     
  Lines         181684    182658      +974     
  Branches       19950     20052      +102     
===============================================
+ Hits          144077    158250    +14173     
+ Misses         30805     17370    -13435     
- Partials        6802      7038      +236     

Impacted Files	Coverage Δ
...efaultGATKVariantAnnotationArgumentCollection.java	100.000% <ø> (ø)
.../annotator/allelespecific/ReducibleAnnotation.java	100.000% <ø> (ø)
...er/tools/walkers/GenotypeGVCFsIntegrationTest.java	90.653% <81.818%> (+89.216%)	:arrow_up:
...titute/hellbender/tools/walkers/GenotypeGVCFs.java	93.243% <88.889%> (-1.672%)	:arrow_down:
...ools/walkers/annotator/VariantAnnotatorEngine.java	87.259% <92.308%> (+0.214%)	:arrow_up:
...ine/GATKPlugin/GATKAnnotationPluginDescriptor.java	79.310% <100.000%> (+0.363%)	:arrow_up:
...ers/GenotypeGVCFsAnnotationArgumentCollection.java	100.000% <100.000%> (ø)
...e/hellbender/utils/variant/GATKVCFHeaderLines.java	95.385% <100.000%> (ø)
...hellbender/tools/walkers/annotator/RawGtCount.java	63.415% <0.000%> (-12.195%)	:arrow_down:
...hellbender/tools/walkers/sv/CollectSVEvidence.java	74.888% <0.000%> (-4.990%)	:arrow_down:
... and 253 more

[samuelklee]

As discussed, let's quickly see if we can generalize this to allow one to specify a set of raw annotations to keep. If it looks like that will be a reach, just let me know and I can go ahead and review. Thanks!

[gatk-bot]

Github actions tests reported job failures from actions build 2921600692 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	11	2921600692.12	logs
integration	8	2921600692.0	logs

[meganshand]

@samuelklee I made an attempt to make the argument more general. It should be ready for review. Thanks!

[samuelklee]

Thanks, @meganshand! Just a heads up, I’m mostly out this week since it’s a vacation week for our daycare. But will try to sneak this in if I can.

[gatk-bot]

Github actions tests reported job failures from actions build 3129008425 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	11	3129008425.12	logs
integration	8	3129008425.0	logs

[gatk-bot]

Github actions tests reported job failures from actions build 3160429275 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	11	3160429275.12	logs
integration	8	3160429275.0	logs

[meganshand]

I think tests are failing only because I changed a header line. I will update the expected VCFs.

[meganshand]

Thanks @cmnbroad, back to you!

[meganshand]

@cmnbroad I think Sam has reviewed the rest of this PR. Thank you for helping me get the argument part working! Assuming tests pass this is ready for a final review.

[samuelklee]

@meganshand you've got a prior approval from me, but let me know if you think I should re-review. Thanks @cmnbroad for helping out with the argument code and reviewing!