Fix getAllowedValuesForDescriptorHelp in GATKAnnotationPluginDescriptor.

[cmnbroad]

Fixes #4875. The newly added test fails without this change. Also opportunistically removed some dead code.

[codecov-io]

Codecov Report

Merging #4876 into master will increase coverage by 0.008%.
The diff coverage is 100%.

@@               Coverage Diff               @@
##              master     #4876       +/-   ##
===============================================
+ Coverage     80.417%   80.425%   +0.008%     
- Complexity     17813     17814        +1     
===============================================
  Files           1089      1089               
  Lines          64133     64133               
  Branches       10340     10340               
===============================================
+ Hits           51574     51579        +5     
+ Misses          8502      8497        -5     
  Partials        4057      4057

Impacted Files	Coverage Δ	Complexity Δ
...ine/GATKPlugin/GATKAnnotationPluginDescriptor.java	76.582% <100%> (+1.266%)	56 <0> (+1)	⬆️
...nder/utils/runtime/StreamingProcessController.java	70.37% <0%> (+0.823%)	50% <0%> (ø)	⬇️
...utils/smithwaterman/SmithWatermanIntelAligner.java	90% <0%> (+10%)	3% <0%> (ø)	⬇️

[jamesemery]

Yeah, this looks like this was one of the API changes to the plugin descriptor that fell through the cracks in Barclay that happened around the time this branch went. We then missed this issue because the descriptor wasn't plugged into anything yet. This looks good 👍 we should probably open a PR to look for any other api incongruities.