Adding oncotator filtering enabled in M2 WDL.

[LeeTL1220]

Fixes #4422

[codecov-io]

Codecov Report

Merging #4423 into master will increase coverage by 0.362%.
The diff coverage is n/a.

@@              Coverage Diff               @@
##             master     #4423       +/-   ##
==============================================
+ Coverage     79.04%   79.402%   +0.362%     
- Complexity    16447     17620     +1173     
==============================================
  Files          1047      1055        +8     
  Lines         59189     63340     +4151     
  Branches       9672     10754     +1082     
==============================================
+ Hits          46783     50293     +3510     
- Misses         8645      9125      +480     
- Partials       3761      3922      +161

Impacted Files	Coverage Δ	Complexity Δ
...titute/hellbender/utils/logging/OneShotLogger.java	78.571% <0%> (-21.429%)	3% <0%> (ø)
...ools/spark/sv/evidence/IntervalCoverageFinder.java	82.222% <0%> (-6.239%)	19% <0%> (+11%)
...er/tools/walkers/annotator/ReadPosRankSumTest.java	94.231% <0%> (-5.769%)	25% <0%> (+15%)
.../DiscoverVariantsFromContigAlignmentsSAMSpark.java	94.872% <0%> (-5.128%)	28% <0%> (+15%)
...ools/walkers/annotator/VariantAnnotatorEngine.java	95.161% <0%> (-2.307%)	111% <0%> (+71%)
...stitute/hellbender/utils/pileup/PileupElement.java	93.939% <0%> (-1.713%)	146% <0%> (+70%)
...dinstitute/hellbender/utils/pileup/ReadPileup.java	90.496% <0%> (-1.45%)	104% <0%> (+40%)
...s/spark/sv/discovery/AnnotatedVariantProducer.java	76.471% <0%> (-1.307%)	23% <0%> (+1%)
...lbender/tools/spark/sv/discovery/SimpleSVType.java	85.393% <0%> (-1.174%)	2% <0%> (ø)
...ecaller/AssemblyBasedCallerArgumentCollection.java	100% <0%> (ø)	1% <0%> (ø)	⬇️
... and 80 more

[LeeTL1220]

@davidbenjamin I also ran an additional test outside of our repo to make sure that this was working properly.

[LeeTL1220]

@brigranger @jnktsj Note when this gets into master and gets released. To keep the previous behavior, you will want to set filter_oncotator_maf to false.

(The default is going to become true, since most cancer analysts will want it this way)

[davidbenjamin]

Looks good!