Eric Coissac
5169f65dc9
Introduce the `obilayeredmap` specification and persistent MPHF-based index architecture for incremental multi-dataset indexing. Implement chunked binary serialization with a fixed `u8` k-mer count limit (256) and overlapping super-kmer segments. Add memory-mapped I/O and a companion `.idx` index file for allocation-free, O(1) unitig access. Update MkDocs navigation, enhance the k-mer comparison script, and add comprehensive tests for serialization, partitioning, and file I/O pipelines.
54 lines
1.4 KiB
YAML
54 lines
1.4 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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- 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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- 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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- obilayeredmap crate: implementation/obilayeredmap.md
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- Architecture:
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- Sequences: architecture/sequences/invariant.md
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watch:
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- docmd
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- mkdocs.yml
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