Prevent close from hiding causal exceptions #528

[lbergelson]

• Exceptions thrown by a tool can be hidden by unsafe close methods throwing additional exceptions.
  Avoid this by making use of try-with-resources suppressed exception handling in order to surface the
  primary exception as well as the secondary ones.

• Fixes Exception in onShutdown mask the actual cause of problems in onStartup. #528

[codecov]

Codecov Report

Merging #7764 (7c3e3a2) into master (110f4f5) will increase coverage by 41.856%.
The diff coverage is 100.000%.

❗ Current head 7c3e3a2 differs from pull request most recent head feb9d08. Consider uploading reports for the commit feb9d08 to get more accurate results

Additional details and impacted files

@@               Coverage Diff                @@
##              master     #7764        +/-   ##
================================================
+ Coverage     45.084%   86.941%   +41.856%     
- Complexity     27429     36867      +9438     
================================================
  Files           2337      2211       -126     
  Lines         182973    173379      -9594     
  Branches       20080     18709      -1371     
================================================
+ Hits           82492    150737     +68245     
+ Misses         94620     16057     -78563     
- Partials        5861      6585       +724     

Impacted Files	Coverage Δ
...stitute/hellbender/cmdline/CommandLineProgram.java	84.810% <100.000%> (+1.584%)	⬆️
...org/broadinstitute/hellbender/engine/GATKTool.java	90.041% <100.000%> (+0.372%)	⬆️
...stitute/hellbender/engine/ReferenceFileSource.java	63.636% <0.000%> (-27.273%)	⬇️
...bender/tools/walkers/vqsr/VariantRecalibrator.java	61.327% <0.000%> (-24.841%)	⬇️
...hellbender/tools/walkers/sv/CollectSVEvidence.java	50.654% <0.000%> (-24.234%)	⬇️
...ute/hellbender/tools/walkers/fasta/ShiftFasta.java	58.586% <0.000%> (-17.172%)	⬇️
...stitute/hellbender/engine/ReferenceDataSource.java	66.667% <0.000%> (-16.667%)	⬇️
...nder/utils/runtime/ProcessControllerAckResult.java	86.364% <0.000%> (-8.373%)	⬇️
...r/arguments/CopyNumberArgumentValidationUtils.java	73.333% <0.000%> (-8.000%)	⬇️
...lbender/tools/walkers/vqsr/VariantDataManager.java	71.660% <0.000%> (-7.287%)	⬇️
... and 1081 more

[droazen]

+1