Eric Coissac
49f329edd5
Exposes RawSnpDistanceOutput and implements KmerIndex::raw_snp_distance() to compute pairwise single-copy locus counts under a paralogy-aware rule. The implementation leverages ndarray for parallel matrix aggregation, producing raw p-distance matrices for sanity-checking. A --raw-snp-distance CLI flag is added to export results as CSV, mapping zero-eligible pairs to NA.
23 lines
568 B
Rust
23 lines
568 B
Rust
pub mod error;
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pub mod meta;
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pub mod state;
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mod distance;
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mod dump;
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mod index;
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mod merge;
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mod numa;
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mod rebuild;
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mod reindex;
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mod select;
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mod siblings;
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mod stats;
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pub use error::{OKIError, OKIResult};
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pub use distance::{DistanceMetric, DistanceOutput};
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pub use index::KmerIndex;
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pub use merge::MergeMode;
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pub use meta::{validate_label, GenomeInfo, IndexConfig, IndexMeta, META_FILENAME};
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pub use state::{IndexState, SENTINEL_COUNTED, SENTINEL_INDEXED, SENTINEL_SCATTERED};
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pub use stats::IndexBitsPerKmer;
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pub use siblings::{RawSnpDistanceOutput, SiblingAnnexStats};
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