VCF Data Sources now preserve FILTER field

[jonn-smith]

No description provided.

[LeeTL1220]

Can you add a test that will produce a VCF with a funcotation annotation and that we can parse it and retrieve the FILTER field?

[LeeTL1220]

Isn't there a VCFConstants constant for this?

[jonn-smith]

Not that I can see. There's one that's close, but contains comments which won't work:

public static final String FILTER_HEADER_START = "##FILTER";

[codecov-io]

Codecov Report

Merging #5598 into master will increase coverage by 0.001%.
The diff coverage is 95.652%.

@@               Coverage Diff               @@
##              master     #5598       +/-   ##
===============================================
+ Coverage     87.047%   87.048%   +0.001%     
- Complexity     31525     31528        +3     
===============================================
  Files           1928      1928               
  Lines         145343    145377       +34     
  Branches       16090     16091        +1     
===============================================
+ Hits          126517    126548       +31     
- Misses         12966     12967        +1     
- Partials        5860      5862        +2

Impacted Files	Coverage Δ	Complexity Δ
...dataSources/vcf/VcfFuncotationFactoryUnitTest.java	98.104% <100%> (+0.055%)	30 <1> (+1)	⬆️
...er/tools/funcotator/FuncotatorIntegrationTest.java	85.253% <100%> (+0.372%)	113 <1> (+1)	⬆️
...cotator/dataSources/vcf/VcfFuncotationFactory.java	88.05% <100%> (+0.469%)	48 <0> (ø)	⬇️
...nder/tools/funcotator/FuncotatorTestConstants.java	98.333% <100%> (+0.028%)	1 <0> (ø)	⬇️
...ute/hellbender/utils/test/FuncotatorTestUtils.java	95.161% <66.667%> (-3.084%)	7 <1> (+1)
...nder/utils/runtime/StreamingProcessController.java	67.299% <0%> (-0.474%)	33% <0%> (ø)

[jonn-smith]

@LeeTL1220 Added in a specific integration test for the FILTER field.

Also rebased on master to fix the unrelated R test failures.