Change VariantEval to not require the output file to already exist.

[cmnbroad]

Fixes #5674. All the tests are written using IntegrationTestSpec which creates the output files before running the test. Verified manually.

[codecov-io]

Codecov Report

Merging #5681 into master will decrease coverage by 0.23%.
The diff coverage is n/a.

@@              Coverage Diff               @@
##              master     #5681      +/-   ##
==============================================
- Coverage     87.043%   86.813%   -0.23%     
- Complexity     31707     31777      +70     
==============================================
  Files           1940      1940              
  Lines         146172    146804     +632     
  Branches       16130     16262     +132     
==============================================
+ Hits          127233    127445     +212     
- Misses         13051     13441     +390     
- Partials        5888      5918      +30

Impacted Files	Coverage Δ	Complexity Δ
...lbender/tools/walkers/varianteval/VariantEval.java	88.04% <ø> (-0.04%)	108 <0> (ø)
...aplotypecaller/HaplotypeCallerIntegrationTest.java	54.457% <0%> (-33.805%)	84% <0%> (ø)
...ls/CalculateGenotypePosteriorsIntegrationTest.java	65.169% <0%> (-29.913%)	13% <0%> (ø)
...iantutils/PosteriorProbabilitiesUtilsUnitTest.java	81.937% <0%> (-9.354%)	35% <0%> (-2%)
...titute/hellbender/engine/AssemblyRegionWalker.java	79.141% <0%> (-7.317%)	39% <0%> (+13%)
...oadinstitute/hellbender/engine/AssemblyRegion.java	80.808% <0%> (-3.688%)	65% <0%> (+17%)
...org/broadinstitute/hellbender/utils/MathUtils.java	77.108% <0%> (-2.492%)	238% <0%> (+18%)
...kers/variantutils/PosteriorProbabilitiesUtils.java	79.091% <0%> (-2.319%)	72% <0%> (+22%)
...ithwaterman/SmithWatermanIntelAlignerUnitTest.java	60% <0%> (ø)	2% <0%> (ø)	⬇️
...nder/utils/runtime/StreamingProcessController.java	67.773% <0%> (+0.474%)	33% <0%> (ø)	⬇️
... and 3 more

[droazen]

@cmnbroad Need one good test, then this can be merged

[droazen]

Can you add at least one test that would have failed without this patch?