removing accidental uses of log4j v1

[lbergelson]

No description provided.

[lbergelson]

This should hopefully resolve the issue discussed here: #5682

[samuelklee]

Looks good, thanks!

[codecov-io]

Codecov Report

Merging #5682 into master will increase coverage by 14.652%.
The diff coverage is 100%.

@@               Coverage Diff               @@
##              master    #5682        +/-   ##
===============================================
+ Coverage     72.397%   87.05%   +14.652%     
- Complexity     26191    31718      +5527     
===============================================
  Files           1940     1940                
  Lines         146204   146204                
  Branches       16134    16134                
===============================================
+ Hits          105848   127270     +21422     
+ Misses         35223    13044     -22179     
- Partials        5133     5890       +757

Impacted Files	Coverage Δ	Complexity Δ
...utils/LeftAlignAndTrimVariantsIntegrationTest.java	100% <ø> (+89.474%)	6 <0> (+5)	⬆️
...cotator/dataSources/vcf/VcfFuncotationFactory.java	88.05% <ø> (+2.516%)	48 <0> (+2)	⬆️
...decs/xsvLocatableTable/XsvLocatableTableCodec.java	81.675% <ø> (+1.571%)	66 <0> (+2)	⬆️
...e/hellbender/tools/funcotator/FuncotatorUtils.java	88.77% <100%> (+4.278%)	193 <3> (+12)	⬆️
...rs/varianteval/evaluators/MultiallelicSummary.java	52.941% <100%> (+52.941%)	8 <1> (+8)	⬆️
...walkers/varianteval/evaluators/VariantSummary.java	84.426% <100%> (+84.426%)	23 <1> (+23)	⬆️
...s/vqsr/VariantRecalibratorModelOutputUnitTest.java	94.245% <100%> (ø)	26 <1> (ø)	⬇️
...s/walkers/varianteval/evaluators/IndelSummary.java	84.416% <100%> (+84.416%)	26 <1> (+26)	⬆️
.../broadinstitute/hellbender/utils/MannWhitneyU.java	93.694% <100%> (ø)	48 <0> (ø)	⬇️
...nteval/stratifications/IntervalStratification.java	71.429% <100%> (+71.429%)	5 <1> (+5)	⬆️
... and 631 more