This commit addresses a bug in the super k-mer implementation where the minimizer bijection property was not properly enforced. The fix ensures that:
1. All k-mers within a super k-mer share the same minimizer
2. Identical super k-mer sequences have the same minimizer
The changes include:
- Fixing the super k-mer iteration logic to properly validate the minimizer bijection property
- Adding a comprehensive test suite (TestSuperKmerMinimizerBijection) that validates the intrinsic property of super k-mers
- Updating the .gitignore file to properly track relevant files
This resolves issues where the same sequence could be associated with different minimizers, violating the super k-mer definition.
This commit adds the implementation of the obisuperkmer command, including:
- The main command in cmd/obitools/obisuperkmer/
- The package implementation in pkg/obitools/obisuperkmer/
- Automated tests in obitests/obitools/obisuperkmer/
- Documentation for the implementation and tests
The obisuperkmer command extracts super k-mers from DNA sequences, following the standard OBITools architecture. It includes proper CLI option handling, validation of parameters, and integration with the OBITools pipeline system.
Tests cover basic functionality, parameter validation, output format, metadata preservation, and file I/O operations.
Ajout d'une documentation détaillée sur l'architecture des commandes OBITools, incluant la structure modulaire, les patterns architecturaux et les bonnes pratiques pour la création de nouvelles commandes.
