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https://github.com/metabarcoding/obitools4.git
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f78543ee75
Refactor k-mer index building to use the new disk-based KmerSetGroupBuilder instead of the old KmerSet and FrequencyFilter approaches. This change introduces a more efficient and scalable approach to building k-mer indices by using partitioned disk storage with streaming operations. - Replace BuildKmerIndex and BuildFrequencyFilterIndex with KmerSetGroupBuilder - Add support for frequency filtering via WithMinFrequency option - Remove deprecated k-mer set persistence methods - Update CLI to use new builder approach - Add new disk-based k-mer operations (union, intersect, difference, quorum) - Introduce KDI (K-mer Delta Index) file format for efficient storage - Add K-way merge operations for combining sorted k-mer streams - Update documentation and examples to reflect new API This refactoring provides better memory usage, faster operations on large datasets, and more flexible k-mer set operations.
37 lines
322 B
Plaintext
37 lines
322 B
Plaintext
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.rhistory
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/.vscode
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/build
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/bugs
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/ncbitaxo
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!/obitests/**
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!/sample/**
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LLM/**
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*_files
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entropy.html
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bug_id.txt
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obilowmask_ref
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test_*
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