Hvcf2gvcf ref allele wrong

[lynnjo]

Description

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Type of change

What type of changes does your code introduce? Put an x in boxes that apply.

• [ ] CHANGE (fix or feature that would cause existing functionality to not work as expected)
• [ ] FEATURE (non-breaking change which adds functionality)
• [x] BUGFIX (non-breaking change which fixes an issue)
• [ ] ENHANCEMENT (non-breaking change which improves existing functionality)
• [ ] NONE (if none of the other choices apply. Example, tooling, build system, CI, docs, etc.)

Checklist:

• [x] I have performed a self-review of my code
• [x] I have commented my code, particularly in hard-to-understand areas
• [ ] I have updated relevant documentation

Changelog entry

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Fixes issue with wrong ref-allele in file created by hvcf2gvcf.

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 75.00000% with 7 lines in your changes missing coverage. Please review.

Project coverage is 83.43%. Comparing base (d2c022f) to head (54dbac0). Report is 25 commits behind head on main.

Files	Patch %	Lines
...in/kotlin/net/maizegenetics/phgv2/cli/Hvcf2Gvcf.kt	68.18%	7 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #201 +/- ## ========================================== + Coverage 83.18% 83.43% +0.25% ========================================== Files 77 77 Lines 5228 5181 -47 Branches 836 835 -1 ========================================== - Hits 4349 4323 -26 + Misses 569 547 -22 - Partials 310 311 +1 ```

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