Eric Coissac
45df9919e5
Introduces a design specification for inferring substitution rates directly from k-mers with conserved flanks. The document details a memory-efficient implementation that computes 4x4 base-pair tallies using existing MPHF structures, enabling classical corrections without de Bruijn graph materialization. Updates MkDocs navigation to include the new theory page.
67 lines
2.2 KiB
YAML
67 lines
2.2 KiB
YAML
site_name: obikmer
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docs_dir: docmd
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site_dir: doc
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theme:
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name: material
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plugins:
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- mermaid2:
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- bibtex:
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bib_file: docmd/references.bib
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csl_file: docmd/ecology-letters.csl
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enable_inline_citations: false
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markdown_extensions:
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- admonition
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- footnotes
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- tables
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- pymdownx.superfences:
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custom_fences:
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- name: mermaid
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class: mermaid
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format: !!python/name:pymdownx.superfences.fence_code_format
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- pymdownx.arithmatex:
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generic: true
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extra_javascript:
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- https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js
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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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- 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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