Integrate CountingVariantFilter.

[cmnbroad]

Fixes #4747.

[codecov-io]

Codecov Report

Merging #4954 into master will decrease coverage by 1.695%.
The diff coverage is 95.238%.

@@               Coverage Diff               @@
##              master     #4954       +/-   ##
===============================================
- Coverage     86.753%   85.058%   -1.695%     
+ Complexity     29767     29142      -625     
===============================================
  Files           1825      1813       -12     
  Lines         137744    137448      -296     
  Branches       15181     15579      +398     
===============================================
- Hits          119497    116910     -2587     
- Misses         12729     15090     +2361     
+ Partials        5518      5448       -70

Impacted Files	Coverage Δ	Complexity Δ
...titute/hellbender/tools/funcotator/Funcotator.java	85.976% <0%> (+0.869%)	46 <1> (+31)	⬆️
...ellbender/tools/walkers/vqsr/CNNScoreVariants.java	75% <0%> (+0.243%)	40 <1> (ø)	⬇️
...der/tools/walkers/variantutils/SelectVariants.java	79.586% <100%> (-0.06%)	115 <3> (-4)
...llbender/engine/filters/VariantFilterUnitTest.java	93.333% <100%> (+3.089%)	10 <4> (+4)	⬆️
...institute/hellbender/engine/VariantWalkerBase.java	100% <100%> (ø)	14 <2> (ø)	⬇️
...ellbender/engine/filters/VariantFilterLibrary.java	90% <100%> (+56.667%)	1 <1> (ø)	⬇️
...titute/hellbender/engine/TwoPassVariantWalker.java	95.238% <100%> (+0.238%)	4 <1> (ø)	⬇️
.../hellbender/tools/walkers/mutect/FilterResult.java	0% <0%> (-100%)	0% <0%> (-7%)
...r/tools/walkers/readorientation/ArtifactPrior.java	0% <0%> (-100%)	0% <0%> (-9%)
...tools/walkers/readorientation/ReadOrientation.java	0% <0%> (-100%)	0% <0%> (-3%)
... and 430 more

[lbergelson]

👍 Looks good to me.

[cmnbroad]

So, the problem with this is that the counting filters use the filter class name to report summaries, and most of the variant filters that we have are implemented using lambdas, so they have no recognizable name. Before this is merged I'll want to reimplement the handful of existing filters used by CNNScoreVariants and Funcotator to use static, named classes in VariantFilterLibrary.

[cmnbroad]

@lbergelson I had to add another commit to this after you reviewed it (see my note above), so back to you for another look.

[lbergelson]

@cmnbroad This looks good to me 👍

[lbergelson]

Looks like this needs a rebase, feel free to merge after unless there are crazy changes needed.