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

OBIKmers/obikmer

T

Eric Coissac f36b095ce2 docs: clarify MPHF indexing, storage layout, and distance traits

Formalize the two-phase MPHF indexing architecture and update Phase 6 to use `evidence.bin` for direct kmer extraction. Simplify the evidence and unitig storage layouts to flat packed formats enabling O(1) random access. Introduce aggregation traits (`ColumnWeights`, `CountPartials`, `BitPartials`) to support additive distance metric decomposition across partitions. Narrow the documented scope from metagenomic to individual genome datasets, and replace speculative open questions with concrete implementation specifications.

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

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

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

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

feat: implement persistent layered index and chunked binary format

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

refactor: delegate MPHF construction and I/O to MphfLayer

2026-05-16 19:32:40 +08:00

.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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