handle negative infinity log likelihoods from Pair-HMM in Mutect2

[davidbenjamin]

@meganshand @ldgauthier This fixes the last homoplasmic missed call in broadinstitute/dsp-spec-ops#116.

[codecov-io]

Codecov Report

Merging #5736 into master will increase coverage by 0.008%.
The diff coverage is 100%.

@@               Coverage Diff               @@
##              master     #5736       +/-   ##
===============================================
+ Coverage     87.067%   87.075%   +0.008%     
- Complexity     31887     31954       +67     
===============================================
  Files           1940      1940               
  Lines         146814    147133      +319     
  Branches       16235     16305       +70     
===============================================
+ Hits          127826    128116      +290     
- Misses         13070     13092       +22     
- Partials        5918      5925        +7

Impacted Files	Coverage Δ	Complexity Δ
...tools/walkers/mutect/SomaticLikelihoodsEngine.java	88.889% <100%> (+1.084%)	18 <4> (+4)	⬆️
...nder/utils/runtime/StreamingProcessController.java	67.299% <0%> (-0.474%)	33% <0%> (ø)
...pecaller/readthreading/ReadThreadingAssembler.java	68.387% <0%> (+0.31%)	66% <0%> (+14%)	⬆️
...aplotypecaller/HaplotypeCallerIntegrationTest.java	89.163% <0%> (+1.232%)	136% <0%> (+49%)	⬆️
...hellbender/utils/pairhmm/VectorLoglessPairHMM.java	86.842% <0%> (+1.316%)	12% <0%> (ø)	⬇️
...oadinstitute/hellbender/utils/pairhmm/PairHMM.java	78.417% <0%> (+3.597%)	24% <0%> (ø)	⬇️
...utils/smithwaterman/SmithWatermanIntelAligner.java	90% <0%> (+10%)	3% <0%> (ø)	⬇️
...ithwaterman/SmithWatermanIntelAlignerUnitTest.java	90% <0%> (+30%)	2% <0%> (ø)	⬇️

[meganshand]

This looks good to me, but do you want me to run this branch on the validation data? Or if Sarah reports back that this fixed the bug for her case, is that good enough?

[davidbenjamin]

@meganshand There's no need to test before merging because this is a bug fix for the edge case of negative infinity log likelihoods from PairHMM, regardless.