CalculateContamination works much better for very small gene panels

[davidbenjamin]

Closes #5821. @bhanugandham With this PR we will no longer have to recommend against using CalculateContamination for gene panels.

@takutosato This puts in a last-ditch calculation that uses hom ref sites and uses sites that didn't get a clear minor allele fraction segmentation. To avoid distorting the signal with LoH hets, it removes the hom ref sites with the highest allele fraction, which will work unless there's a huge amount of CNV. This will result in a slight underestimate, but for a small gene panel there's not much you can do.

[codecov-io]

Codecov Report

Merging #5873 into master will increase coverage by 0.089%.
The diff coverage is 50%.

@@               Coverage Diff               @@
##              master     #5873       +/-   ##
===============================================
+ Coverage     86.838%   86.927%   +0.089%     
- Complexity     32274     32928      +654     
===============================================
  Files           1987      1987               
  Lines         149001    150609     +1608     
  Branches       16469     16840      +371     
===============================================
+ Hits          129390    130920     +1530     
- Misses         13598     13637       +39     
- Partials        6013      6052       +39

Impacted Files	Coverage Δ	Complexity Δ
...pecaller/readthreading/ReadThreadingAssembler.java	68.077% <ø> (ø)	52 <0> (ø)	⬇️
...ools/walkers/contamination/ContaminationModel.java	87.5% <50%> (-4.891%)	39 <9> (ø)
...llbender/engine/spark/SparkCommandLineProgram.java	89.474% <0%> (-3.383%)	7% <0%> (+2%)
...tools/walkers/mutect/SomaticLikelihoodsEngine.java	91.045% <0%> (-1.978%)	31% <0%> (+13%)
...alkers/mutect/SomaticReferenceConfidenceModel.java	95.122% <0%> (-1.753%)	16% <0%> (+8%)
.../broadinstitute/hellbender/utils/QualityUtils.java	84.848% <0%> (-0.517%)	25% <0%> (+11%)
.../mutect/filtering/M2FiltersArgumentCollection.java	94.203% <0%> (-0.392%)	12% <0%> (+6%)
...ller/ReadThreadingAssemblerArgumentCollection.java	96.078% <0%> (-0.075%)	3% <0%> (+1%)
...walkers/mutect/clustering/BetaBinomialCluster.java	100% <0%> (ø)	20% <0%> (+10%)	⬆️
...er/tools/walkers/mutect/Mutect2EngineUnitTest.java	100% <0%> (ø)	10% <0%> (+5%)	⬆️
... and 28 more

[takutosato]

Looks good!