Eric Coissac
ea914bb536
Introduce the siblingannex module in obicompactvec to store per-slot minorant flags and sibling counts in a memory-mapped annex file. Add a scatter-gather pipeline in obikindex to compute these values across index layers and write them to .psib files. Implement central_canonical_neighbors in obikseq for generating strand-aware k-mer variants around the middle base. Expose rolling statistics in obiskbuilder and update dependency graphs accordingly.
44 lines
1.0 KiB
Rust
44 lines
1.0 KiB
Rust
//! Super-kmer construction pipeline.
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//!
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//! Consumes normalised rope chunks from `obiread` and produces
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//! `(minimizer, SuperKmer)` pairs ready for scatter routing.
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#![deny(missing_docs)]
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pub mod iter;
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pub mod stream_iter;
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mod scratch;
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pub(crate) mod encoding;
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#[allow(missing_docs)]
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pub mod rolling_stat;
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pub use iter::SuperKmerIter;
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pub use scratch::SuperKmerScratch;
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pub use stream_iter::SuperKmerStreamIter;
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use obiread::NucPage;
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use obikrope::Rope;
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use obikseq::RoutableSuperKmer;
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/// Collect all super-kmers from a normalised [`NucPage`].
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pub fn build_superkmers_page(
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page: NucPage,
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k: usize,
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level_max: usize,
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theta: f64,
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) -> Vec<RoutableSuperKmer> {
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let cursor = page.cursor();
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SuperKmerStreamIter::new(cursor, k, level_max, theta).collect()
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}
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/// Collect all super-kmers from a normalised rope chunk.
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pub fn build_superkmers(
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rope: Rope,
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k: usize,
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level_max: usize,
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theta: f64,
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) -> Vec<RoutableSuperKmer> {
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SuperKmerIter::new(&rope, k, level_max, theta).collect()
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}
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