Add site ID to VCF output

[roohy]

Description

I added modified to python/tskit/vcf.py file to write the site ID of the variant in the ID field of the VCF file output.
I added a test to check VCF variant ID and site ID in the ts object are the same in test_vcf.py file under the TestInterface class just in case. I did not add anything to documentation or the changelogs since I first wanted to submit this draft pull request and ask first since the change is very minimal.
Fixes #2103

PR Checklist:

• [ ✅] Tests that fully cover new/changed functionality.

[codecov]

Codecov Report

Merging #2107 (92e7125) into main (f950e34) will increase coverage by 0.00%.
The diff coverage is 100.00%.

❗ Current head 92e7125 differs from pull request most recent head fb29186. Consider uploading reports for the commit fb29186 to get more accurate results

@@           Coverage Diff           @@
##             main    #2107   +/-   ##
=======================================
  Coverage   93.37%   93.37%           
=======================================
  Files          27       27           
  Lines       25586    25587    +1     
  Branches     1159     1159           
=======================================
+ Hits        23890    23891    +1     
  Misses       1666     1666           
  Partials       30       30           

Flag	Coverage Δ
c-tests	92.34% <ø> (ø)
lwt-tests	89.05% <ø> (ø)
python-c-tests	72.12% <0.00%> (-0.01%)	⬇️
python-tests	98.89% <100.00%> (+<0.01%)	⬆️

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Impacted Files	Coverage Δ
python/tskit/trees.py	98.05% <ø> (ø)
python/tskit/vcf.py	100.00% <100.00%> (ø)

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[roohy]

Hi,
The error in the test process is raised by the mismatch between the VCF file with ID columns and the function 'legacy_write_vcf' which is implemented in the test_vcf.py to ensure compatibility with previous versions (there is also a minor Pylint issue). Is it OK if I change that function?

[benjeffery]

Thanks for the PR @roohy! Will review today.

[benjeffery]

Great! Thanks @roohy!
I've made one small suggestion to simplify the testing.
Please go ahead and add a changelog and a note in the docs.

[roohy]

Changelog and docs added.

[benjeffery]

Changelog and docs added.

Great, thanks. All that is left is to fix the failing test (tests/test_vcf.py::TestLegacyOutput) and run the linting pre-commit run --all. I can do those bits if you like?

[roohy]

Thank you! I tried doing them so as not to take any more of your time. Please let me know if I am still forgetting something.

[benjeffery]

I've squashed and rebased.
Thanks for this @roohy, great to have you on the contributors list.

[roohy]

Thanks @benjeffery for your help. I hope I can make more/bigger contributions to your great software in the future!