obitools4

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Commit Graph

Author	SHA1	Message	Date
Eric Coissac	7a979ba77f	Add obisuperkmer command implementation and tests 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.	2026-02-07 13:54:02 +01:00
Eric Coissac	00c8be6b48	docs: add architecture documentation for OBITools commands 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.	2026-02-07 12:26:35 +01:00
Eric Coissac	500144051a	Add jj Makefile targets and k-mer encoding utilities Add new Makefile targets for jj operations (jjnew, jjpush, jjfetch) to streamline commit workflow. Introduce k-mer encoding utilities in pkg/obikmer: - EncodeKmers: converts DNA sequences to encoded k-mers - ReverseComplement: computes reverse complement of k-mers - NormalizeKmer: returns canonical form of k-mers - EncodeNormalizedKmers: encodes sequences with normalized k-mers Add comprehensive tests for k-mer encoding functions including edge cases, buffer reuse, and performance benchmarks. Document k-mer index design for large genomes, covering: - Use cases and objectives - Volume estimations - Distance metrics (Jaccard, Sørensen-Dice, Bray-Curtis) - Indexing options (Bloom filters, sorted sets, MPHF) - Optimization techniques (k-2-mer indexing) - MinHash for distance acceleration - Recommended architecture for presence/absence and counting queries	2026-02-04 14:27:10 +01:00

Author

SHA1

Message

Date

Eric Coissac

7a979ba77f

Add obisuperkmer command implementation and tests

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.

2026-02-07 13:54:02 +01:00

Eric Coissac

00c8be6b48

docs: add architecture documentation for OBITools commands

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.

2026-02-07 12:26:35 +01:00

Eric Coissac

500144051a

Add jj Makefile targets and k-mer encoding utilities

Add new Makefile targets for jj operations (jjnew, jjpush, jjfetch) to streamline commit workflow.

Introduce k-mer encoding utilities in pkg/obikmer:
- EncodeKmers: converts DNA sequences to encoded k-mers
- ReverseComplement: computes reverse complement of k-mers
- NormalizeKmer: returns canonical form of k-mers
- EncodeNormalizedKmers: encodes sequences with normalized k-mers

Add comprehensive tests for k-mer encoding functions including edge cases, buffer reuse, and performance benchmarks.

Document k-mer index design for large genomes, covering:
- Use cases and objectives
- Volume estimations
- Distance metrics (Jaccard, Sørensen-Dice, Bray-Curtis)
- Indexing options (Bloom filters, sorted sets, MPHF)
- Optimization techniques (k-2-mer indexing)
- MinHash for distance acceleration
- Recommended architecture for presence/absence and counting queries

2026-02-04 14:27:10 +01:00

3 Commits