[jonas-fuchs]

This release fixes duplicate variant calls from overlapping feature matches and simplifies how the CLI selects rule-backed features. Generated profile plots also get a small readability update.

New features:

None.

Bug fixes:

• VCF remapping now collapses duplicate variants projected to the same location and alleles from overlapping matches, keeping the best-scoring match. It also ties each query codon to the feature alignment that produced it, preventing codon-frame leakage between overlapping features.

Improvements:

• Feature selection now uses a persisted has_rules flag and a rules-only alignment approach instead of suppressing ruleless overlapping features after annotation. Existing project databases are migrated automatically.
• Profile plots use smaller, angled labels and slightly wider jitter spacing to improve readability.

Breaking changes:

None.

[codecov]

Codecov Report

❌ Patch coverage is 96.61017% with 2 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
respro/core/vcf_remap.py	96.55%	0 Missing and 1 partial ⚠️
respro/db/rules_import.py	83.33%	0 Missing and 1 partial ⚠️

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