rust-ise 0.2.3

Fast Rust-native ISEScan-equivalent insertion-sequence (IS) scanner for bacterial (meta)genomes: rustygal ORFs + MMseqs2 profile search + native affine-SW terminal inverted repeats.
Documentation 
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[package]
name = "rust-ise"
version = "0.2.3"
edition = "2021"
rust-version = "1.74"
authors = ["Sunju Kim <n.e.coli.1822@gmail.com>"]
description = "Fast Rust-native ISEScan-equivalent insertion-sequence (IS) scanner for bacterial (meta)genomes: rustygal ORFs + MMseqs2 profile search + native affine-SW terminal inverted repeats."
license = "GPL-3.0-or-later"
readme = "README.md"
repository = "https://github.com/necoli1822/rust-ise"
homepage = "https://github.com/necoli1822/rust-ise"
keywords = ["bioinformatics", "insertion-sequence", "metagenomics", "transposon", "genomics"]
categories = ["science", "command-line-utilities"]
# Keep dev/output artifacts and the maintainer deploy checklist out of the package.
exclude = [
    "out_*", "*.time", "target", "compare_*.py", "run_*.sh", "*_results.tsv",
    "DEPLOY_TASKS.md",
]

[lib]
name = "rust_ise"
path = "src/lib.rs"

[[bin]]
name = "rust-ise"
path = "src/main.rs"

[dependencies]
rayon = "1.10"
# rustygal META gene-finding, linked as a library (rust-pure; no external rustygal binary).
# Published crates.io dependency (0.2.0 has the meta_api module build-db uses; 0.1.0 predates it).
# For a local side-by-side checkout, override with `[patch.crates-io] rustygal = { path = "…" }`.
rustygal = "0.2.0"
# Compile-time perfect-hash map of per-profile pident thresholds (data/rep_thresholds.tsv),
# embedded in the binary (GTDB-calibrated; gates contaminant/promiscuous profiles at search time).
phf = "0.11"
# `build-db` subcommand only: in-process partial-order multiple sequence alignment (pure Rust),
# replacing the reference pipeline's external clustalo. Not used by the scanner (`rust_ise::run`).
poasta = "0.1.0"
# `build-db --fetch-sources` only: sha256 verification of pinned source downloads and
# in-process extraction of ISOSDB.V3.fna.zip (both pure Rust; downloads use system curl).
sha2 = "0.10"
zip = { version = "0.6", default-features = false, features = ["deflate"] }
# NB (runtime, NOT cargo deps): `mmseqs` must be on PATH; the IS DB is provided via --db / $ISSCAN_DB.
# `build-db` additionally shells out to `mmseqs` (cluster + msa2profile + createdb); no other external tools.

[build-dependencies]
phf_codegen = "0.11"

[profile.release]
lto = "fat"
codegen-units = 1
opt-level = 3

[workspace]