Eric Coissac
f7ebc7a1ab
Introduce a design specification outlining performance bottlenecks in layer data access and an agreed-upon implementation direction for caching. Refactor the codebase to centralize index and layer directory path resolution within the partition object, replacing manual string joining and external helper functions with dedicated accessor methods.
70 lines
2.4 KiB
YAML
70 lines
2.4 KiB
YAML
site_name: obikmer
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bib_file: DevDocMD/references.bib
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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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- "Benchmark: query-path testing": implementation/benchmark_query_testing.md
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- "Partition and layer caching (discussion)": implementation/partition_layer_cache.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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- DevDocMD
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- mkdocs.yml
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