deacon 0.14.0

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# See Cargo.toml.orig for the original contents.

[package]
edition = "2024"
name = "deacon"
version = "0.14.0"
authors = ["Bede Constantinides <b@bede.im>"]
build = false
exclude = [
    "bench/*",
    "data/*",
]
autolib = false
autobins = false
autoexamples = false
autotests = false
autobenches = false
description = "Accelerated DNA sequence search and [host] depletion using minimizers"
homepage = "https://github.com/bede/deacon"
readme = "README.md"
keywords = [
    "bioinformatics",
    "genomics",
    "filtering",
    "decontamination",
]
categories = [
    "science",
    "command-line-utilities",
]
license = "MIT"
repository = "https://github.com/bede/deacon"

[features]
compression = [
    "zstd",
    "liblzma",
    "flate2",
    "gzp",
    "needletail/compression",
    "paraseq/default",
]
default = [
    "compression",
    "fetch",
]
fetch = ["minreq"]
gz = [
    "niffler/gz",
    "flate2",
    "flate2/default",
]

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

[[bin]]
name = "deacon"
path = "src/main.rs"

[[test]]
name = "cli_tests"
path = "tests/cli_tests.rs"

[[test]]
name = "filter_tests"
path = "tests/filter_tests.rs"

[[test]]
name = "index_tests"
path = "tests/index_tests.rs"

[dependencies.anyhow]
version = "1.0"

[dependencies.bincode]
version = "2.0"
features = ["serde"]

[dependencies.clap]
version = "4.5"
features = ["derive"]

[dependencies.ensure_simd]
version = "0.1.0"

[dependencies.flate2]
version = "1.1"
features = ["zlib-rs"]
optional = true

[dependencies.gzp]
version = "2.0"
features = ["deflate_rust"]
optional = true
default-features = false

[dependencies.indicatif]
version = "0.18"

[dependencies.liblzma]
version = "0.3"
optional = true

[dependencies.minreq]
version = "2"
features = ["https-rustls-probe"]
optional = true

[dependencies.needletail]
version = "0.6"
default-features = false

[dependencies.niffler]
version = "3"
default-features = false

[dependencies.packed-seq]
version = "4.2.0"

[dependencies.paraseq]
version = "0.4.3"
features = [
    "anyhow",
    "niffler",
]
default-features = false

[dependencies.parking_lot]
version = "0.12"

[dependencies.rand]
version = "0.9"

[dependencies.rapidhash]
version = "4.1.0"

[dependencies.rayon]
version = "1"

[dependencies.serde]
version = "1.0"
features = ["derive"]

[dependencies.serde_json]
version = "1.0"

[dependencies.simd-minimizers]
version = "2.2.0"

[dependencies.thiserror]
version = "2.0"

[dependencies.zstd]
version = "0.13"
optional = true

[dev-dependencies.assert_cmd]
version = "2.0"

[dev-dependencies.nix]
version = "0.30"
features = ["fs"]

[dev-dependencies.predicates]
version = "3.0"

[dev-dependencies.rstest]
version = "0.26"

[dev-dependencies.tempfile]
version = "3.20"

[lints.clippy]
too_many_arguments = "allow"

[profile.dist]
inherits = "release"

[profile.release]
opt-level = 3
lto = true
codegen-units = 1
debug = 0
panic = "abort"
strip = false