Mutect3 dataset enhancements: optional truth VCF for labels, seq error likelihood annotation

[davidbenjamin]

No description provided.

[davidbenjamin]

@meganshand Would you mind reviewing this PR, which will enable M3 testing on Ultima? To the extent your conscience permits it really only needs a rubber stamp. No one besides me is familiar with the M3 code and while that is eventually worth addressing I don't think you or anyone else should be responsible for increasing the M3 bus factor until it is more stable.

[codecov]

Codecov Report

Merging #7975 (9fd8de7) into master (8d81423) will decrease coverage by 0.001%.
The diff coverage is 63.636%.

@@               Coverage Diff               @@
##              master     #7975       +/-   ##
===============================================
- Coverage     86.679%   86.679%   -0.001%     
  Complexity     38455     38455               
===============================================
  Files           2310      2310               
  Lines         180387    180401       +14     
  Branches       19845     19848        +3     
===============================================
+ Hits          156358    156369       +11     
- Misses         17087     17088        +1     
- Partials        6942      6944        +2     

Impacted Files	Coverage Δ
...der/tools/walkers/mutect/M2ArgumentCollection.java	95.000% <ø> (ø)
...der/tools/walkers/mutect/Mutect3DatasetEngine.java	87.786% <63.158%> (-2.130%)	⬇️
.../tools/walkers/mutect/SomaticGenotypingEngine.java	93.617% <66.667%> (-0.469%)	⬇️
.../hellbender/utils/python/PythonUnitTestRunner.java	78.689% <0.000%> (+3.279%)	⬆️

[meganshand]

Thanks @davidbenjamin! Looks good 👍

[davidbenjamin]

Thanks @meganshand!