Support fasta.gz in GATKSparkTool

[tomwhite]

Fixes #5258

[codecov-io]

Codecov Report

Merging #5290 into master will increase coverage by <.01%.
The diff coverage is 100%.

@@             Coverage Diff              @@
##             master    #5290      +/-   ##
============================================
+ Coverage     86.77%   86.77%   +<.01%     
  Complexity    29888    29888              
============================================
  Files          1834     1834              
  Lines        138473   138479       +6     
  Branches      15241    15242       +1     
============================================
+ Hits         120162   120170       +8     
+ Misses        12760    12758       -2     
  Partials       5551     5551

Impacted Files	Coverage Δ	Complexity Δ
...stitute/hellbender/engine/spark/GATKSparkTool.java	82.19% <100%> (+0.37%)	68 <0> (ø)	⬇️
...ls/spark/BaseRecalibratorSparkIntegrationTest.java	40.54% <100%> (+1.09%)	5 <0> (ø)	⬇️
...va/org/broadinstitute/hellbender/GATKBaseTest.java	100% <100%> (ø)	7 <0> (ø)	⬇️
...e/hellbender/engine/spark/SparkContextFactory.java	73.97% <0%> (+2.73%)	11% <0%> (ø)	⬇️

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[lbergelson]

@tomwhite Thank you. This looks good to me.