Crate sshash_lib 

sshash-lib

Core library for SSHash-rs: a compressed k-mer dictionary based on sparse and skew hashing.

Quick Start

use sshash_lib::{Dictionary, Kmer, KmerBits};

type Kmer31 = Kmer<31>;

fn main() -> Result<(), Box<dyn std::error::Error>> {
    // Load a previously built index
    let dict = Dictionary::load("index")?;

    // Single k-mer lookup (returns position or INVALID_UINT64)
    let kmer = Kmer31::from_string("ACGTACGTACGTACGTACGTACGTACGTACG")?;
    let pos = dict.lookup::<31>(&kmer);

    // Streaming queries over a sequence
    let mut engine = dict.create_streaming_query::<31>();

    Ok(())
}

Modules

Module	Purpose
dictionary	Load, save, lookup, and query k-mers
builder	Index construction pipeline
streaming_query	Efficient sequential k-mer processing
kmer	Kmer<K> with const-generic sizing and bit-parallel ops
minimizer	Minimizer extraction and iteration
minimizers_control_map	MPHF-based minimizer→bucket mapping
spectrum_preserving_string_set	SPSS: unitig storage and position lookup
sparse_and_skew_index	Bucket dispatch (singleton / light / heavy)
offsets	Elias-Fano encoded string boundary offsets

License

MIT

Re-exports

pub use kmer::Kmer;

pub use kmer::Kmer21;

pub use kmer::Kmer31;

pub use kmer::Kmer63;

pub use kmer::KmerBits;

pub use minimizer::MinimizerInfo;

pub use minimizer::MinimizerIterator;

pub use minimizers_control_map::MinimizersControlMap;

pub use minimizers_control_map::MinimizersControlMapBuilder;

pub use minimizers_control_map::BucketType;

pub use streaming_query::LookupResult;

pub use streaming_query::StreamingQuery;

pub use dictionary::Dictionary;

pub use builder::BuildConfiguration;

pub use builder::CfSegData;

pub use builder::DictionaryBuilder;

pub use builder::parse_cf_seg;

pub use partitioned_mphf::PartitionedMphf;

Modules

builder

Builder module for constructing SSHash dictionaries

constants

Constants and configuration for SSHash

dictionary

Dictionary - the main SSHash data structure

encoding

DNA nucleotide encoding

hasher

Deterministic hasher for minimizers using rapidhash.

kmer

K-mer representation with const generics and optimal storage

minimizer

Minimizer extraction and iteration

minimizers_control_map

Minimizers Control Map (MCM)

mphf_config

MPHF (Minimal Perfect Hash Function) type configuration

offsets

Compact encoding of offsets into a bit-packed string set

partitioned_mphf

Partitioned Minimal Perfect Hash Function

serialization

Serialization and deserialization support for Dictionary

sparse_and_skew_index

Sparse and Skew Index for k-mer lookup

spectrum_preserving_string_set

Spectrum-Preserving String Set (SPSS)

streaming_query

Streaming query for efficient k-mer lookups

Macros

dispatch_on_k

Dispatch to the correct const generic K based on a runtime k value.

Functions

version

Version information