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OBIKmers/obikmer

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Eric Coissac 13599dd444 feat: Implement query subcommand for sequence-to-genome mapping

This change introduces the `query` CLI command and its supporting infrastructure for sequence-to-genome mapping and k-mer matching. It adds a `QueryLayer` abstraction backed by MPHF and persistent matrices, exposes the index partition for direct querying, and implements `Hash`/`Eq` for `RoutableSuperKmer`. The command ingests sequence batches, deduplicates superkmers, routes them to index partitions for parallel exact or 1-mismatch matching, and outputs results as FASTA records annotated with JSON metadata. Includes `serde_json` dependency addition, module exports, and documentation updates.

2026-05-21 18:56:41 +02:00

harden obiskio error handling with explicit variants and bounds checking

2026-05-09 18:30:19 +08:00

refactor: implement RoutableSuperKmer and update k-mer indexing pipeline

2026-05-01 09:33:26 +02:00

first implementation but far to be optimal

2026-04-19 12:17:16 +02:00

docs: clarify MPHF indexing, storage layout, and distance traits

2026-05-17 15:59:10 +08:00

feat: Implement query subcommand for sequence-to-genome mapping

2026-05-21 18:56:41 +02:00

refactor: restructure k-mer partitioning pipeline for memory efficiency

2026-05-17 16:08:47 +08:00

feat: implement persistent layered index and chunked binary format

2026-05-09 17:38:29 +08:00

feat: Implement query subcommand for sequence-to-genome mapping

2026-05-21 18:56:41 +02:00

.DS_Store

feat(obikmer): add index subcommand for kmer counting pipeline

2026-05-20 18:25:12 +02:00

.gitignore

refactor: implement RoutableSuperKmer and update k-mer indexing pipeline

2026-05-01 09:33:26 +02:00

Cargo.lock

first implementation but far to be optimal

2026-04-19 12:17:16 +02:00

CLAUDE.md

feat: add kmer iterators and optimize layered map performance

2026-05-12 22:35:21 +08:00

debug.log

Refactor: Extract utility function for string reversal

2026-04-30 06:58:46 +02:00

kmer_spectrum_raw.json

refactor: implement RoutableSuperKmer and update k-mer indexing pipeline

2026-05-01 09:33:26 +02:00

Makefile

Refactor: Simplify user authentication flow

2026-04-28 08:38:26 +02:00

mkdocs.yml

feat: add merge command to consolidate k-mer indexes

2026-05-21 13:44:50 +02:00

obikmer 2026-05-20 12.53 profile.json.gz

feat(obikmer): add index subcommand for kmer counting pipeline

2026-05-20 18:25:12 +02:00

profile.json.gz

Refactor: Simplify user authentication flow

2026-04-28 08:38:26 +02:00

README.md

first implementation but far to be optimal

2026-04-19 12:17:16 +02:00

test.sk.fasta

first implementation but far to be optimal

2026-04-19 12:17:16 +02:00

TODO.md

feat: Implement query subcommand for sequence-to-genome mapping

2026-05-21 18:56:41 +02:00

xxx.HTML

first implementation but far to be optimal

2026-04-19 12:17:16 +02:00

README.md

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v1.3.5

Latest

2026-09-12 05:49:49 +00:00

HTML 52.6%

Rust 42.5%

Python 1.7%

Shell 1.2%

Makefile 1%

Other 1%