Crate gtars_refget 

Rust implementation of GA4GH Refget sequence collection functions

This module provides functions managing and retrieving sequences from a sequence collection.

Module Structure

The library is organized into two main parts:

Core (WASM-compatible)

The digest module contains all WASM-compatible code:

• digest::algorithms - Hash functions (sha512t24u, md5, canonicalize_json)
• digest::alphabet - Sequence alphabets and encoding tables
• digest::encoder - Sequence bit-packing
• digest::types - Core data structures (SequenceRecord, SequenceCollection)
• digest::fasta - Bytes-based FASTA parsing
• digest::stream - Streaming FASTA hasher for chunk-by-chunk processing

Filesystem (requires filesystem feature)

• fasta - File-based FASTA parsing (wraps digest::fasta with file I/O)
• collection - Extended SequenceCollection with filesystem operations
• store - RefgetStore for persistent sequence storage

Feature Flags

• filesystem (default): Enables file-based operations
• Without filesystem: Only WASM-compatible code in digest module

Re-exports

pub use digest::ASCII_ALPHABET;

pub use digest::Alphabet;

pub use digest::AlphabetGuesser;

pub use digest::AlphabetType;

pub use digest::DNA_2BIT_ALPHABET;

pub use digest::DNA_3BIT_ALPHABET;

pub use digest::DNA_IUPAC_ALPHABET;

pub use digest::FaiMetadata;

pub use digest::FastaStreamHasher;

pub use digest::PROTEIN_ALPHABET;

pub use digest::ParseOptions;

pub use digest::SeqColDigestLvl1;

pub use digest::SequenceCollection;

pub use digest::SequenceCollectionMetadata;

pub use digest::SequenceCollectionRecord;

pub use digest::SequenceEncoder;

pub use digest::SequenceMetadata;

pub use digest::SequenceRecord;

pub use digest::canonicalize_json;

pub use digest::decode_string_from_bytes;

pub use digest::decode_substring_from_bytes;

pub use digest::digest_fasta_bytes;

pub use digest::digest_sequence;

pub use digest::digest_sequence_with_description;

pub use digest::encode_sequence;

pub use digest::guess_alphabet;

pub use digest::load_fasta_bytes;

pub use digest::lookup_alphabet;

pub use digest::md5;

pub use digest::parse_fasta_header;

pub use digest::parse_rgsi_line;

pub use digest::sha512t24u;

pub use collection::SequenceCollectionExt;

pub use collection::SequenceCollectionRecordExt;

pub use collection::SequenceMetadataExt;

pub use collection::SequenceRecordExt;

pub use collection::read_rgsi_file;

pub use fasta::FaiRecord;

pub use fasta::compute_fai;

pub use fasta::digest_fasta;

pub use fasta::load_fasta;

Modules

collection

Extended SequenceCollection with filesystem operations. Adds methods for RGSI file I/O, caching, and file-based construction. Extended SequenceCollection with filesystem operations.

digest

Core digest and encoding functionality - WASM-safe. All code in this module works without filesystem access. Core digest and encoding functionality - WASM-safe.

fasta

File-based FASTA operations. Wraps the WASM-compatible digest::fasta with filesystem I/O. File-based FASTA operations.

store

Persistent sequence storage (RefgetStore).