Eric Coissac
1881e98bad
Introduces `partial_jaccard_dist` to return raw intersection and union counts, improving Jaccard distance flexibility. Corrects `not()` to explicitly zero padding bits in the final word, ensuring accurate bit-counting for partially-filled words. Adds an optimized `build_from_counts` constructor.
57 lines
1.6 KiB
YAML
57 lines
1.6 KiB
YAML
site_name: obikmer
|
|
docs_dir: docmd
|
|
site_dir: doc
|
|
|
|
theme:
|
|
name: material
|
|
|
|
plugins:
|
|
- mermaid2:
|
|
- bibtex:
|
|
bib_file: docmd/references.bib
|
|
csl_file: docmd/ecology-letters.csl
|
|
enable_inline_citations: false
|
|
|
|
markdown_extensions:
|
|
- admonition
|
|
- footnotes
|
|
- tables
|
|
- pymdownx.superfences:
|
|
custom_fences:
|
|
- name: mermaid
|
|
class: mermaid
|
|
format: !!python/name:pymdownx.superfences.fence_code_format
|
|
- pymdownx.arithmatex:
|
|
generic: true
|
|
|
|
extra_javascript:
|
|
- https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js
|
|
|
|
nav:
|
|
- Home: index.md
|
|
- Theory:
|
|
- Kmers and super-kmers: kmers.md
|
|
- DNA encoding: theory/encoding.md
|
|
- Entropy filter: theory/entropy.md
|
|
- Minimizer selection: theory/minimizer.md
|
|
- Partitioning architecture: theory/indexing.md
|
|
- Implementation:
|
|
- SuperKmer: implementation/superkmer.md
|
|
- Kmer: implementation/kmer.md
|
|
- Chunk reader: implementation/chunkreader.md
|
|
- Construction pipeline: implementation/pipeline.md
|
|
- obipipeline library: implementation/obipipeline.md
|
|
- On-disk storage: implementation/storage.md
|
|
- MPHF selection: implementation/mphf.md
|
|
- Unitig evidence encoding: implementation/unitig_evidence.md
|
|
- obilayeredmap crate: implementation/obilayeredmap.md
|
|
- PersistentCompactIntVec: implementation/persistent_compact_int_vec.md
|
|
- PersistentBitVec: implementation/persistent_bit_vec.md
|
|
- Architecture:
|
|
- Sequences: architecture/sequences/invariant.md
|
|
- Kmer index: architecture/index_architecture.md
|
|
|
|
watch:
|
|
- docmd
|
|
- mkdocs.yml
|