Multi-Allelic Variant Funcotation Filtration

[tlangs]

Since Funcotation annotation can be multi-allelic, the filtration code needs to not assume that all Funcotated variants will have only one key of each funcotation.

[codecov-io]

Codecov Report

Merging #5588 into master will decrease coverage by 0.029%.
The diff coverage is 90.244%.

@@               Coverage Diff               @@
##              master     #5588       +/-   ##
===============================================
- Coverage     87.041%   87.012%   -0.029%     
- Complexity     31490     31795      +305     
===============================================
  Files           1924      1940       +16     
  Lines         145189    146481     +1292     
  Branches       16082     16198      +116     
===============================================
+ Hits          126374    127456     +1082     
- Misses         12958     13108      +150     
- Partials        5857      5917       +60

Impacted Files	Coverage Δ	Complexity Δ
...er/tools/funcotator/filtrationRules/LofFilter.java	100% <100%> (ø)	5 <2> (ø)	⬇️
...ools/funcotator/filtrationRules/ClinVarFilter.java	100% <100%> (ø)	7 <5> (+2)	⬆️
...er/tools/funcotator/filtrationRules/LmmFilter.java	100% <100%> (ø)	3 <2> (+1)	⬆️
...ellbender/tools/funcotator/FilterFuncotations.java	93.103% <100%> (ø)	18 <1> (ø)	⬇️
.../funcotator/filtrationRules/FuncotationFilter.java	100% <100%> (ø)	8 <4> (+4)	⬆️
...r/filtrationRules/FilterFuncotationsExacUtils.java	81.818% <80.952%> (-0.535%)	12 <7> (+5)
...walkers/genotyper/afcalc/AFCalculatorProvider.java	22.222% <0%> (-44.444%)	2% <0%> (-2%)
...notyper/afcalc/ConcurrentAFCalculatorProvider.java	50% <0%> (-33.333%)	1% <0%> (-1%)
...nder/utils/downsampling/PositionalDownsampler.java	88.462% <0%> (-11.538%)	22% <0%> (+1%)
...er/engine/spark/datasources/VariantsSparkSink.java	78.125% <0%> (-11.53%)	8% <0%> (-1%)
... and 138 more

[lbergelson]

@jonn-smith Looks like this is for you, or to delegate as you please.

[jonn-smith]

Looks good.

I have a minor request and a question.

[jonn-smith]

Looks good!