upgrading to spark 2.2.0

[lbergelson]

This bumped some transitive dependencies which required a minor update in unrelated classes

We shouldn't merge this until we get a 👍 from the SV team as well as running the jenkins spark tests.

I think the SV team is already using 2.2.0 since they've gone to dataproc image 1.2.

This will prevent the annoying adam log spam, closes #4186
closes #2555

[lbergelson]

This is exploding due to netty conflicts between version 4.0.4x and 4.1.x. I'm not sure why the move to spark 2.2.0 changed this exactly, but the version that causes problem is imported by google's gatk-java library. Removing that removes the conflict. I rebased this ontop of the branch I have in PR that removes that library and hopefully it won't fail...

[codecov-io]

Codecov Report

Merging #4314 into master will decrease coverage by 0.007%.
The diff coverage is 100%.

@@               Coverage Diff               @@
##              master     #4314       +/-   ##
===============================================
- Coverage     79.024%   79.017%   -0.007%     
+ Complexity     16447     16440        -7     
===============================================
  Files           1047      1047               
  Lines          59186     59186               
  Branches        9672      9672               
===============================================
- Hits           46771     46767        -4     
- Misses          8659      8661        +2     
- Partials        3756      3758        +2

Impacted Files	Coverage Δ	Complexity Δ
...tute/hellbender/utils/report/GATKReportColumn.java	90% <100%> (ø)	22 <4> (ø)	⬇️
...utils/smithwaterman/SmithWatermanIntelAligner.java	50% <0%> (-30%)	1% <0%> (-2%)
...ender/tools/spark/sv/evidence/KmerAndInterval.java	89.474% <0%> (-5.263%)	11% <0%> (-1%)
...te/hellbender/tools/spark/sv/utils/SVKmerLong.java	92.308% <0%> (-1.538%)	28% <0%> (-1%)
...lbender/utils/read/SAMRecordToGATKReadAdapter.java	92.032% <0%> (-0.398%)	134% <0%> (-1%)
...park/sv/discovery/alignment/AlignmentInterval.java	89.272% <0%> (ø)	73% <0%> (ø)	⬇️
...nder/utils/runtime/StreamingProcessController.java	71.193% <0%> (+0.823%)	51% <0%> (+1%)	⬆️

[droazen]

👍 merge once #4266 is merged, you've rebased this branch on top of it, and tests pass in both travis and jenkins

[droazen]

@lbergelson How's this one looking? Can it be merged yet?

[droazen]

@lbergelson Are you comfortable merging this one yet?

[droazen]

@lbergelson As part of your current set of Spark test runs, can you also test whether this PR appears to work on dataproc?