fixes bug in gga mode caused by split multallic sites with genotypes

[cwhelan]

Fixes #5355.

Another issue caused by creating a new variant context from an existing one with new alleles, but having the old alleles persist because the genotypes were not reset.

[codecov-io]

Codecov Report

Merging #5365 into master will increase coverage by 1.163%.
The diff coverage is 100%.

@@               Coverage Diff               @@
##              master     #5365       +/-   ##
===============================================
+ Coverage     85.745%   86.909%   +1.163%     
- Complexity     30028     30314      +286     
===============================================
  Files           1849      1849               
  Lines         140507    140513        +6     
  Branches       15475     15475               
===============================================
+ Hits          120478    122118     +1640     
+ Misses         14480     12786     -1694     
- Partials        5549      5609       +60

Impacted Files	Coverage Δ	Complexity Δ
...r/AssemblyBasedCallerGenotypingEngineUnitTest.java	100% <100%> (ø)	31 <0> (ø)	⬇️
...ypecaller/AssemblyBasedCallerGenotypingEngine.java	89.45% <100%> (+0.049%)	89 <0> (+1)	⬆️
...stitute/hellbender/cmdline/CommandLineProgram.java	83.117% <0%> (+1.948%)	43% <0%> (+1%)	⬆️
...stitute/hellbender/utils/config/ConfigFactory.java	76.398% <0%> (+3.727%)	45% <0%> (+2%)	⬆️
...r/arguments/CopyNumberArgumentValidationUtils.java	77.778% <0%> (+6.173%)	20% <0%> (+1%)	⬆️
...tute/hellbender/utils/runtime/ProcessSettings.java	93.75% <0%> (+6.25%)	18% <0%> (+2%)	⬆️
...te/hellbender/utils/python/PythonExecutorBase.java	73.333% <0%> (+6.667%)	4% <0%> (+2%)	⬆️
...er/utils/runtime/CapturedStreamOutputSnapshot.java	78.571% <0%> (+7.143%)	4% <0%> (+1%)	⬆️
...lbender/utils/io/HardThresholdingOutputStream.java	80% <0%> (+10%)	4% <0%> (+1%)	⬆️
...itute/hellbender/utils/runtime/ScriptExecutor.java	81.25% <0%> (+14.583%)	10% <0%> (+3%)	⬆️
... and 38 more

[ldgauthier]

👍