Eric Coissac
5c1584967f
The command now supports reopening existing indexes instead of failing when the output file exists. Control flow branches between opening an existing index and constructing a new one, moving configuration setup exclusively to the creation path. Directory existence is enforced upfront with proper I/O error propagation. The --force flag retains its original semantics by removing the target directory before proceeding with a fresh build.
70 lines
2.4 KiB
YAML
70 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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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: DevDocMD/references.bib
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csl_file: DevDocMD/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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- obikindex layer tier: implementation/layer_tier.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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