Refactor GVCFWriter to allow push/pull iteration.

[tomwhite]

This is @lbergelson's work from https://github.com/broadinstitute/gatk/compare/lb_updates_for_haplotype_caller, rebased for master. It is needed for #5138.

[lbergelson]

Laura made changes to the gvcf writer which I think we'll have to update here.. since I wrote this way before then.

[tomwhite]

I rebased to take care of these changes (from #4940) - there were quite a few manual changes needed.

[lbergelson]

Ah, that makes sense since otherwise the tests should be exploding. I just wanted to be sure about it...

[codecov-io]

Codecov Report

Merging #5311 into master will increase coverage by 0.004%.
The diff coverage is 92.486%.

@@               Coverage Diff               @@
##              master     #5311       +/-   ##
===============================================
+ Coverage     86.984%   86.988%   +0.004%     
- Complexity     31208     31224       +16     
===============================================
  Files           1909      1914        +5     
  Lines         144202    144264       +62     
  Branches       15954     15956        +2     
===============================================
+ Hits          125433    125492       +59     
- Misses         12999     13003        +4     
+ Partials        5770      5769        -1

Impacted Files	Coverage Δ	Complexity Δ
...ellbender/utils/iterators/PushPullTransformer.java	0% <0%> (ø)	0 <0> (?)
...ls/variant/writers/GVCFBlockCombiningIterator.java	0% <0%> (ø)	0 <0> (?)
...ute/hellbender/utils/downsampling/Downsampler.java	100% <100%> (ø)	6 <1> (ø)	⬇️
...hellbender/utils/iterators/PushToPullIterator.java	100% <100%> (ø)	17 <17> (?)
.../utils/downsampling/ReadsDownsamplingIterator.java	100% <100%> (ø)	1 <1> (-16)	⬇️
...e/hellbender/utils/variant/writers/GVCFWriter.java	100% <100%> (+6.667%)	8 <6> (-26)	⬇️
...nder/utils/variant/writers/GVCFWriterUnitTest.java	96.796% <80%> (+0.007%)	48 <1> (ø)	⬇️
...ender/utils/variant/writers/GVCFBlockCombiner.java	93.182% <93.182%> (ø)	35 <35> (?)
...er/utils/iterators/PushToPullIteratorUnitTest.java	97.059% <97.059%> (ø)	6 <6> (?)
... and 5 more

[droazen]

@tomwhite Apologies for not getting around to this one before leaving, but rather than keep it blocked while I'm away I'm re-assigning to @cmnbroad, who I'm sure can give you a speedy review.
My main comment from glancing at the code is that the new PushPullTransformer and PushToPullIterator classes lack direct unit tests.

[tomwhite]

@droazen @cmnbroad thanks for taking a look. I've added some direct unit tests for PushPullTransformer and PushToPullIterator.

[cmnbroad]

A few comments and questions. Also, although ideally GVCFBlockCombiner would have separate unit tests, it appears to have 100% coverage through GVCFWriterUnitTest. Finally, @ldgauthier FWIW note this is going to create conflicts with your changes in #5312.

[tomwhite]

Thanks for your review @cmnbroad. I've addressed all your points. Please approve so this can be merged.

[cmnbroad]

Looks good now thx @tomwhite.

[tomwhite]

Thank you @cmnbroad!