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.
1049 lines
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Kmers and super-kmers
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DNA encoding
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Minimizer selection
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Partitioning architecture
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SuperKmer
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Kmer
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Chunk reader
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Construction pipeline
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obipipeline library
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On-disk storage
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MPHF selection
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Unitig evidence encoding
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obilayeredmap crate
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PersistentCompactIntVec
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PersistentBitVec
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Kmer index
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<h1 id="obikmer">obikmer</h1>
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<p><code>obikmer</code> is a Rust tool for manipulation, counting, indexing, and set operations on DNA sequences represented as kmer sets.</p>
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<h2 id="constraints">Constraints</h2>
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<ul>
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<li>Target scale: individual genome datasets, tens of Gbases</li>
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<li>Maximum efficiency in computation, memory, and disk usage</li>
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<li>Input formats: FASTA, FASTQ, gzip, streaming stdin</li>
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</ul>
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<h2 id="priority-operations">Priority operations</h2>
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<ul>
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<li>Kmer counting (frequencies)</li>
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<li>Fast search / query</li>
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<li>Set operations: union, intersection, difference</li>
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