Rust crates and executables

The compute-heavy stages run in six Rust crates under rust/. Each crate has its own README with the exact command lines, and --help on every executable is the authoritative option list. The Python package finds the executables through an explicit path, FASTALAKE_BIN_DIR, the repository build directories, and then PATH (see Environment).

Crate	Executables	Stage	README
fasta_extractor_v2	fasta_extractor, lake_builder, hash_fasta, fasta_sort_by_id, mass_kmer_anchor, mass_corasick, mass_corasick_v2, mass_corasick_v3, parsimony	Reference lake (stage 0), pooled and per-acquisition evidence extraction (stages 1 and 2), mass-tolerant rescue	fasta_extractor_v2, parameters
parsimony_engine	parsimony_engine	Protein inference (stage 3): razor and the alternative strategies	parsimony_engine
aggregation_engine	aggregation_engine	Cross-acquisition matrices from Sage output (stage 5)	aggregation_engine
fasta_export	fasta_export	Engine-aware FASTA export and entrapment FDP from Sage results	fasta_export
shared_peptide_classifier	shared_peptide_classifier	UNIQUE or SHARED calls for rescued peptides, consumed by parsimony_engine --weights	shared_peptide_classifier
lake_stats	lake_stats	Tryptic peptide-space saturation of a FASTA	lake_stats

Build

The toolchain is pinned in rust-toolchain.toml; every crate has a Cargo.lock. The three crates the study runner needs:

for crate in fasta_extractor_v2 parsimony_engine aggregation_engine; do
  cargo build --release --locked --manifest-path "rust/$crate/Cargo.toml"
done

Continuous integration runs cargo fmt --check, cargo clippy -D warnings, cargo test and cargo deny for all six crates on every push. The Docker image contains release builds of all of them.

Determinism

Every executable writes its outputs in a fixed order, independent of thread count and directory listing order, so identical inputs give byte-identical files. The algorithms page states the tie rules that make this possible.