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OBIKmers/obikmer

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Eric Coissac bc51cd9861 feat: add configurable block sizes and in-place reindex command

Propagate configurable block size (`block_bits`) through index and layer construction to control unitig chunking and optimize memory/performance trade-offs. Introduce an in-place `reindex` command and library method to convert indices between exact and approximate evidence formats. Add validation to reject merging indexes with mismatched evidence types, and update parallel kmer counting to use `AtomicUsize` for thread-safe aggregation. Includes CLI argument parsing, metadata persistence, and updated tests.

2026-05-23 13:28:24 +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 configurable block sizes and in-place reindex command

2026-05-23 13:28:24 +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: add evidence metadata and configurable k-mer parameters

2026-05-23 13:10:18 +02:00

xxx.HTML

first implementation but far to be optimal

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

README.md

toto

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%