Eric Coissac
f36b095ce2
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.
16 lines
452 B
Markdown
16 lines
452 B
Markdown
# obikmer
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`obikmer` is a Rust tool for manipulation, counting, indexing, and set operations on DNA sequences represented as kmer sets.
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## Constraints
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- Target scale: individual genome datasets, tens of Gbases
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- Maximum efficiency in computation, memory, and disk usage
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- Input formats: FASTA, FASTQ, gzip, streaming stdin
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## Priority operations
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- Kmer counting (frequencies)
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- Fast search / query
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- Set operations: union, intersection, difference
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