Eric Coissac
b1f54b7d2f
Introduces batch retrieval and sub-matrix extraction methods across vector, view, reader, and matrix types. These implementations optimize cache locality by sorting requested indices for sequential memory access before applying an inverse permutation to restore original order. Includes allocation-free variants that populate caller-provided buffers. Updates architecture documentation to define sibling annex persistence in iteration order and clarify pipeline separation.
68 lines
2.3 KiB
YAML
68 lines
2.3 KiB
YAML
site_name: obikmer
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site_dir: doc
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bib_file: docmd/references.bib
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csl_file: docmd/ecology-letters.csl
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nav:
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- Home: index.md
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- Installation: installation.md
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- Theory:
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- Kmers and super-kmers: kmers.md
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- DNA encoding: theory/encoding.md
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- Entropy filter: theory/entropy.md
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- Minimizer selection: theory/minimizer.md
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- Partitioning architecture: theory/indexing.md
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- Central-position SNP distance (discussion): theory/evolutionary_distances.md
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- Implementation:
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- SuperKmer: implementation/superkmer.md
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- Kmer: implementation/kmer.md
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- Chunk reader: implementation/chunkreader.md
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- Construction pipeline: implementation/pipeline.md
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- obipipeline library: implementation/obipipeline.md
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- On-disk storage: implementation/storage.md
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- MPHF selection: implementation/mphf.md
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- Unitig evidence encoding: implementation/unitig_evidence.md
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- Evidence elimination (discussion): implementation/evidence_elimination.md
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- obilayeredmap crate: implementation/obilayeredmap.md
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- PersistentCompactIntVec: implementation/persistent_compact_int_vec.md
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- PersistentBitVec: implementation/persistent_bit_vec.md
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- Merge command: implementation/merge.md
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- Merge parallelism & memory: implementation/merge_parallelism.md
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- Kmer filtering: implementation/filtering.md
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- Select command: implementation/select.md
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- obitaxonomy crate: implementation/obitaxonomy.md
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- Architecture:
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- Sequences: architecture/sequences/invariant.md
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- Kmer index: architecture/index_architecture.md
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- Sibling annex (discussion): architecture/siblings.md
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- NUMA-aware worker pools: architecture/numa_worker_pools.md
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- NUMA-aware partition runner: architecture/numa_partition_runner.md
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watch:
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- docmd
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- mkdocs.yml
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