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

OBIKmers/obikmer

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Eric Coissac b80ab77d66 perf: Switch to sequential PHF construction to avoid thread contention

The outer partition loop already saturates parallelism, making parallel PHF construction redundant and causing Rayon thread pool contention. This change switches to a sequential variant to improve performance. Additionally, explicit error handling is now added for construction failures, while preserving the existing mmap-backed kmer slice.

2026-05-20 12:48:42 +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

refactor: restructure k-mer partitioning pipeline for memory efficiency

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

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

perf: Switch to sequential PHF construction to avoid thread contention

2026-05-20 12:48:42 +02:00

.DS_Store

feat: add obilayeredmap crate for disk-backed k-mer indexing

2026-05-12 15:26:39 +08:00

.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(bitvec): add partial Jaccard, fix padding, optimize constructor

2026-05-15 15:04:10 +08:00

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

Add persistent compact integer vector and cache-line-optimized MPHF

2026-05-13 10:09:46 +08:00

xxx.HTML

first implementation but far to be optimal

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

README.md

toto

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