OBIKmers/obikmer - obikmer - Gitea: Git with a cup of tea

OBIKmers/obikmer

T

Eric Coissac e1dab86daf feat: add approximate kmer fingerprinting with memory-mapped storage

Introduce a new `fingerprint` module that stores packed B-bit vectors via memory-mapped files. Expose the module publicly and add `build_approx_evidence` to `Layer` and `MphfLayer` for generating compact `fingerprint.bin` files. Implement `find_approx` for fast, probabilistic kmer lookups using configurable bit-widths. Update dependencies to `bitvec` v1 and add `cacheline-ef`, `epserde`, and `memmap2` to support the new storage and serialization logic.

2026-05-23 13:07:02 +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: optimize unitig index and document evidence elimination

2026-05-23 12:53:42 +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: add approximate kmer fingerprinting with memory-mapped storage

2026-05-23 13:07:02 +02:00

.DS_Store

feat: introduce genome metadata tracking and CSV export

2026-05-22 09:35:20 +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: optimize unitig index and document evidence elimination

2026-05-23 12:53:42 +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

toto

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