Handling of applied variants with and without modifications

[trishorts]

Few things here:

1. Simple expansion of some unit tests to better reveal current behavior for the treatment of sequence variants that are supported by VCF data.
2. Homozygous variants with depth greater than specified results in only the production of the variant protein or RNA. you do not get the consensus protein or RNA in that case. This was a surprise.
3. List of sequence variants in proteins and RNAs wasn't properly adjust when variants get applied. Desired behavior is to remove applied variants from the sequence variants list when they get applied.
4. This PR helps display proper handling of modifications on variants.

[Copilot]

Pull Request Overview

This PR enhances the variant modification system by explicitly separating unapplied database sequence variants from applied sequence variants. The key improvement is that applied variants are now removed from the SequenceVariations collection and tracked separately in AppliedSequenceVariations, providing clearer representation of variant state throughout the codebase.

Key changes:

• Modified CreateVariant signatures to accept both sequenceVariants (database variants) and appliedSequenceVariants parameters
• Implemented logic to remove applied variants from SequenceVariations collection in variant construction
• Updated all test assertions to reflect the new behavior where variants with applied sequence variations have empty SequenceVariations lists

Reviewed Changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
mzLib/Transcriptomics/RNA.cs	Added overloaded constructor with explicit sequenceVariants parameter and removal logic for applied variants
mzLib/Transcriptomics/NucleicAcid.cs	Updated abstract CreateVariant signature to include sequenceVariants parameter
mzLib/Proteomics/Protein/Protein.cs	Updated CreateVariant implementation with variant removal logic matching RNA implementation
mzLib/Omics/BioPolymer/VariantApplication.cs	Modified variant application logic to pass database variants explicitly through construction chain
mzLib/Omics/BioPolymer/IHasSequenceVariants.cs	Updated interface signature and documentation for CreateVariant method
mzLib/Test/Transcriptomics/TestVariantOligo.cs	Updated test assertions to expect 0 unapplied variants after application; split test cases and added documentation
mzLib/Test/DatabaseTests/TestVariantProtein.cs	Updated test assertions and added comprehensive test for VCF variant with modifications
mzLib/Test/Test.csproj	Added new test data file to project
mzLib/Test/DatabaseTests/oneVcfProteinWithModsOnVariant.xml	New test data file for VCF variant testing

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[Copilot]

Corrected XML comment closing tag from '// ' to '/// '.

Suggested change

	// </summary>
	/// </summary>

[codecov]

Codecov Report

❌ Patch coverage is 96.82540% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 81.01%. Comparing base (57f1327) to head (8c67a7c).

⚠️ Current head 8c67a7c differs from pull request most recent head c503815

Please upload reports for the commit c503815 to get more accurate results.

Files with missing lines	Patch %	Lines
mzLib/Proteomics/Protein/Protein.cs	93.33%	0 Missing and 1 partial ⚠️
mzLib/Transcriptomics/RNA.cs	96.77%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #974      +/-   ##
==========================================
+ Coverage   81.00%   81.01%   +0.01%     
==========================================
  Files         269      269              
  Lines       38826    38869      +43     
  Branches     4241     4247       +6     
==========================================
+ Hits        31450    31490      +40     
  Misses       6640     6640              
- Partials      736      739       +3     

Files with missing lines	Coverage Δ
mzLib/Omics/BioPolymer/VariantApplication.cs	82.44% <100.00%> (+0.67%)	⬆️
mzLib/Transcriptomics/NucleicAcid.cs	94.83% <ø> (ø)
mzLib/Proteomics/Protein/Protein.cs	97.11% <93.33%> (-0.31%)	⬇️
mzLib/Transcriptomics/RNA.cs	98.18% <96.77%> (-1.82%)	⬇️

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[Copilot]

Pull Request Overview

Copilot reviewed 9 out of 9 changed files in this pull request and generated no new comments.

Comments suppressed due to low confidence (1)

mzLib/Test/DatabaseTests/TestVariantProtein.cs:1

• The test attribute [Test] is missing from this test method. Without it, the test will not be executed by the test runner.

using System;

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