fix(lapis): advanced queries: allow ambiguous mutation symbols in "mutation from", disallow . and - in insertions

[fengelniederhammer]

resolves #1508

Changes the grammar of the advances queries:

• allow ambiguous symbols in "mutation from", e.g. those are allowed now:
  • N501G
  • gene:X501T
• disallow . ("equal to reference") and - ("deletion") in insertions, e.g. those will error now:
  • ins_501:A.A
  • ins_gene:501:A-A

I also restructured one of the unit tests to make it easier to maintain.

PR Checklist

- [ ] All necessary documentation has been adapted. not necessary as far as I can see

• The implemented feature is covered by an appropriate test.

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Project	Deployment	Actions	Updated (UTC)
lapis	Ready	Preview, Comment	Feb 19, 2026 10:26am

[Copilot]

Pull request overview

This PR enhances mutation query handling in Lapis by allowing ambiguous IUPAC codes in the "mutation from" position and restricting special symbols (. and -) from being used in insertions and "mutation from" positions. The changes update the ANTLR grammar, add ambiguous amino acid codes B and Z, and refactor tests from individual methods to a parameterized test structure.

Changes:

• Extended ambiguous amino acid symbols to include B (Aspartic acid/Asparagine) and Z (Glutamic acid/Glutamine) in addition to X
• Modified ANTLR grammar to allow ambiguous symbols in "from" position while disallowing . and - in insertions and "from" positions
• Refactored mutation and insertion tests from individual test methods to comprehensive parameterized test cases using TestCaseCollection

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
lapis/src/main/antlr/org/genspectrum/lapis/model/advancedqueryparser/AdvancedQuery.g4	Restructured grammar rules to merge ambiguous symbols into main symbol rules and created specialSymbolsInMutationTo for . and -
lapis/src/main/kotlin/org/genspectrum/lapis/model/MutationValidator.kt	Added B and Z to ambiguousAaSymbols set for proper IUPAC amino acid ambiguity code support
lapis/src/main/kotlin/org/genspectrum/lapis/model/AdvancedQueryCustomListener.kt	Simplified variable naming in mutation handling logic for better code clarity
lapis/src/test/kotlin/org/genspectrum/lapis/model/AdvancedQueryFacadeTest.kt	Refactored individual test methods into comprehensive TestCaseCollection-based parameterized tests with extensive coverage
lapis/src/test/kotlin/org/genspectrum/lapis/model/AdvancedQueryFacadeMultiSegmentTest.kt	Added tests verifying ambiguous symbols work correctly in multi-segmented genomes

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