Eric Coissac
036d044291
Refactor `Kmer`, `SuperKmer`, and chunk reader into optimized, generic representations with compile-time length parameters and bitwise operations. Update the pipeline and scheduler to support batch processing, 1→N flat transformations, and multi-source merging. Introduce an approximate evidence mode using b-bit fingerprints and `.idx` files, alongside existing exact mode. Update CLI documentation, minimizer selection, and query output schema accordingly.
1.6 KiB
1.6 KiB
obikmer
obikmer is a Rust tool for manipulation, counting, indexing, and set operations on DNA sequences represented as kmer sets.
Subcommands
| Subcommand | Purpose |
|---|---|
superkmer |
Extract super-kmers from a sequence file and write to stdout |
index |
Build a complete genome index (scatter → dereplicate → count → layered MPHF) |
merge |
Merge multiple built indexes into one |
rebuild |
Filter and compact an existing index into a new single-layer index |
query |
Query an index with sequences and annotate matches |
dump |
Dump all indexed kmers as CSV (kmer + per-genome counts or presence) |
annotate |
Add or update genome metadata from a CSV file; or dump metadata as CSV |
distance |
Compute pairwise distance matrix between genomes; optionally build NJ/UPGMA trees |
unitig |
Dump unitigs from a built index to stdout (debug) |
estimate |
Estimate approximate-index parameters (z, evidence bits, FP rates) before indexing |
reindex |
Convert an index's evidence in-place: exact ↔ approx |
Constraints
- Target scale: individual genome datasets, tens of Gbases
- Maximum efficiency in computation, memory, and disk usage
- k odd, k ∈ [11, 31], fixed at runtime; kmer fits in a u64 (2 bits/base)
- Canonical form:
min(kmer, revcomp(kmer))reduces strand-symmetric space by half - Input formats: FASTA, FASTQ, gzip, streaming stdin
Priority operations
- Kmer counting (frequencies)
- Fast search / query
- Set operations: union, intersection, difference