Eric Coissac
89ea077456
Introduces a complete query benchmark track to evaluate performance and verify consistency between dense and sparse index formats. Adds scripts to simulate fixed-size paired-end reads, pack a sparse presence index, execute queries in both modes, and capture wall time and RSS metrics. Includes a verification step that compares outputs by read ID to ensure content identity across parallel processing. Updates build configuration, documentation, and ignore patterns to support the new pipeline for two microbial specimens.
69 lines
2.4 KiB
YAML
69 lines
2.4 KiB
YAML
site_name: obikmer
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docs_dir: DevDocMD
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site_dir: DevDoc
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bib_file: DevDocMD/references.bib
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csl_file: DevDocMD/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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- "Benchmark: query-path testing": implementation/benchmark_query_testing.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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