Fixed issue causing VariantRecalibrator to sometimes fail if user provides duplicate -an options

[KevinCLydon]

Modified VariantRecalibrator to only use a deduped version of the annotations list provided by the user once the list has been deduped. Previously it was still sometimes using the list that could have duplicates

Fixes #8226

Also fixed the logger warning that prints the duplicate annotations.

[ldgauthier]

Very elegant. I guess I missed this case when I did the .distinct() bugfix a while ago.

[codecov]

Codecov Report

Merging #8227 (e0f07ef) into master (24f62de) will increase coverage by 0.000%.
The diff coverage is 90.000%.

Additional details and impacted files

@@             Coverage Diff             @@
##              master     #8227   +/-   ##
===========================================
  Coverage     86.654%   86.655%           
  Complexity     39168     39168           
===========================================
  Files           2346      2346           
  Lines         183670    183675    +5     
  Branches       20152     20152           
===========================================
+ Hits          159158    159163    +5     
- Misses         17449     17451    +2     
+ Partials        7063      7061    -2     

Impacted Files	Coverage Δ
...bender/tools/walkers/vqsr/VariantRecalibrator.java	86.168% <66.667%> (ø)
...lbender/tools/walkers/vqsr/VariantDataManager.java	78.947% <100.000%> (ø)
...lkers/vqsr/VariantRecalibratorIntegrationTest.java	98.361% <100.000%> (+0.046%)	⬆️
...itute/hellbender/tools/LocalAssemblerUnitTest.java	92.448% <0.000%> (ø)