Turn off tranches plots if no output Rscript is specified (for annota…

[ldgauthier]

…tion plots)

Should prevent VariantRecalibrator from failing in a docker without R. I tested by building a new docker from the image with the NIO fix, adding a jar from this branch, then running the SNPSVariantRecalibratorCreateModel task from the joint calling pipeline.

[ldgauthier]

@droazen Here's the fix, but I'm only about 99.6% sure the tests will pass, so don't merge yet.

[codecov-io]

Codecov Report

Merging #3383 into master will decrease coverage by 0.025%.
The diff coverage is 0%.

@@               Coverage Diff               @@
##              master     #3383       +/-   ##
===============================================
- Coverage     80.492%   80.467%   -0.025%     
+ Complexity     17511     17507        -4     
===============================================
  Files           1173      1173               
  Lines          63375     63376        +1     
  Branches        9877      9878        +1     
===============================================
- Hits           51012     50997       -15     
- Misses          8413      8431       +18     
+ Partials        3950      3948        -2

Impacted Files	Coverage Δ	Complexity Δ
...bender/tools/walkers/vqsr/VariantRecalibrator.java	59.367% <0%> (-1.364%)	58 <0> (ø)
...g/broadinstitute/hellbender/utils/io/Resource.java	42.857% <0%> (-9.524%)	4% <0%> (-1%)
...dinstitute/hellbender/utils/R/RScriptExecutor.java	84.694% <0%> (-6.122%)	23% <0%> (-3%)
...e/hellbender/engine/spark/SparkContextFactory.java	66.667% <0%> (-3.333%)	10% <0%> (ø)

[eitanbanks]

works for me