Use allele info in VariantContext comparisons for stable sorts

[clintval]

TLDR: This PR will make coordinate VCF sorting in HTSJDK/Picard similar to bcftools.

I tried to use Picard's SortVcf for a VCF comparison task, but I had difficulty because it's output was non-stable based on the full primary information of a variant context (contig, start, and alleles). I finally chose the bcftools implementation because it has a slightly more-stable sorting method. However, I want to ensure future users of Picard don't hit the same issue I did, hence this PR.

Before I write unit tests, is this something you are willing to accept?

[codecov-commenter]

Codecov Report

Merging #1593 (2272c16) into master (b5af659) will decrease coverage by 0.064%. The diff coverage is 0.000%.

:exclamation: Current head 2272c16 differs from pull request most recent head 5089e22. Consider uploading reports for the commit 5089e22 to get more accurate results

@@               Coverage Diff               @@
##              master     #1593       +/-   ##
===============================================
- Coverage     69.839%   69.775%   -0.064%     
+ Complexity      9647      9641        -6     
===============================================
  Files            702       702               
  Lines          37638     37535      -103     
  Branches        6113      6080       -33     
===============================================
- Hits           26286     26190       -96     
+ Misses          8903      8888       -15     
- Partials        2449      2457        +8     

Impacted Files	Coverage Δ
...riant/variantcontext/VariantContextComparator.java	0.000% <0.000%> (ø)
...htsjdk/samtools/util/nio/DeleteOnExitPathHook.java	80.952% <0.000%> (-9.524%)	:arrow_down:
...sjdk/samtools/util/htsget/HtsgetErrorResponse.java	73.333% <0.000%> (-6.667%)	:arrow_down:
...tools/cram/encoding/core/GammaIntegerEncoding.java	86.667% <0.000%> (-6.667%)	:arrow_down:
.../samtools/cram/compression/ExternalCompressor.java	69.565% <0.000%> (-4.509%)	:arrow_down:
...mtools/cram/encoding/core/BetaIntegerEncoding.java	91.304% <0.000%> (-4.348%)	:arrow_down:
...am/encoding/core/CanonicalHuffmanByteEncoding.java	52.941% <0.000%> (-2.941%)	:arrow_down:
...ing/core/huffmanUtils/HuffmanParamsCalculator.java	80.000% <0.000%> (-1.818%)	:arrow_down:
...va/htsjdk/samtools/util/htsget/HtsgetResponse.java	89.394% <0.000%> (-1.783%)	:arrow_down:
...java/htsjdk/beta/codecs/variants/vcf/VCFCodec.java	81.818% <0.000%> (-1.515%)	:arrow_down:
... and 39 more

[clintval]

Any interest from the maintainers in this PR?

Anything I can do to help move it closer to merge?

[clintval]

@cmnbroad I hit another instance where this would have helped me.

Do you want me to invest the time to implement some unit tests, or is there no interest in pursuing this PR?

[cmnbroad]

@clintval Stable sounds good to me, but @lbergelson who is out on vacation really needs to weigh in (I'm not actually a maintainer).

[lbergelson]

@clintval I'm sorry I haven't been responsive. This is a good idea and having some tests would be great.

[clintval]

@lbergelson I don't normally write in Java so I hope my last commits are OK!

[clintval]

@lbergelson nice work and thank you kindly for the review!