Mutect2 uses natural logarithms internally

[davidbenjamin]

This does not change any outputs or inputs, which remain log-10.

@takutosato I ran the DREAM challenges before and after and the vcfs are identical. Besides replacing log10 methods with log methods I moved some things from MathUtils to NaturaLogUtils for clarity.

[codecov-io]

Codecov Report

Merging #5858 into master will increase coverage by 0.208%.
The diff coverage is 94.177%.

@@               Coverage Diff               @@
##              master     #5858       +/-   ##
===============================================
+ Coverage     86.851%   87.059%   +0.208%     
- Complexity     32121     32220       +99     
===============================================
  Files           1984      1985        +1     
  Lines         147583    147611       +28     
  Branches       16227     16230        +3     
===============================================
+ Hits          128178    128509      +331     
+ Misses         13512     13174      -338     
- Partials        5893      5928       +35

Impacted Files	Coverage Δ	Complexity Δ
.../broadinstitute/hellbender/utils/QualityUtils.java	85.366% <ø> (ø)	14 <0> (ø)	⬇️
...ute/hellbender/utils/variant/GATKVCFConstants.java	75% <ø> (ø)	4 <0> (ø)	⬇️
...utectReadThreadingAssemblerArgumentCollection.java	70% <ø> (ø)	2 <0> (ø)	⬇️
...ols/walkers/mutect/clustering/SequencingError.java	60% <ø> (ø)	3 <0> (ø)	⬇️
...allerReadThreadingAssemblerArgumentCollection.java	71.429% <ø> (ø)	3 <0> (ø)	⬇️
...dinstitute/hellbender/utils/MathUtilsUnitTest.java	92.448% <100%> (-0.068%)	150 <2> (-2)
...tils/variant/writers/SomaticGVCFBlockCombiner.java	90.476% <100%> (ø)	12 <1> (ø)	⬇️
...r/tools/walkers/mutect/Mutect2IntegrationTest.java	87.776% <100%> (ø)	91 <0> (ø)	⬇️
...e/hellbender/utils/variant/GATKVCFHeaderLines.java	94.886% <100%> (ø)	11 <0> (ø)	⬇️
...der/tools/walkers/CombineGVCFsIntegrationTest.java	89.905% <100%> (ø)	38 <0> (ø)	⬇️
... and 70 more