Fix log4j logging which was broken due to multiple copies being prese…

[tomwhite]

…nt on the classpath. Fixes #2622.

[codecov-io]

Codecov Report

Merging #3652 into master will increase coverage by 0.012%.
The diff coverage is n/a.

@@               Coverage Diff               @@
##              master     #3652       +/-   ##
===============================================
+ Coverage     79.384%   79.396%   +0.012%     
- Complexity     17292     17324       +32     
===============================================
  Files           1140      1140               
  Lines          62494     62575       +81     
  Branches        9489      9494        +5     
===============================================
+ Hits           49610     49682       +72     
- Misses          9108      9112        +4     
- Partials        3776      3781        +5

Impacted Files	Coverage Δ	Complexity Δ
...e/hellbender/engine/spark/SparkContextFactory.java	71.233% <0%> (-2.74%)	11% <0%> (ø)
...der/tools/walkers/contamination/PileupSummary.java	90.196% <0%> (-1.232%)	24% <0%> (+10%)
...ools/walkers/contamination/GetPileupSummaries.java	88.235% <0%> (-0.954%)	22% <0%> (+9%)
...er/tools/spark/sv/discovery/AlignmentInterval.java	89.212% <0%> (ø)	64% <0%> (ø)	⬇️
.../walkers/contamination/CalculateContamination.java	89.552% <0%> (+0.663%)	37% <0%> (+13%)	⬆️
...oadinstitute/hellbender/utils/gcs/BucketUtils.java	79.87% <0%> (+1.299%)	39% <0%> (ø)	⬇️

[lbergelson]

👍 we may want to figure out a more permanent solution to this at some point or it's going to keep sneaking back in

[lbergelson]

@tomwhite Thank you!