deacon 0.13.2

Fast DNA search and [host] depletion using minimizers
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[[bin]]
name = "deacon"
path = "src/main.rs"

[dependencies.anyhow]
version = "1.0"

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

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

[dependencies.ensure_simd]
version = "0.1.0"

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

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

[dependencies.indicatif]
version = "0.18"

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

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

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

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

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

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

[dependencies.parking_lot]
version = "0.12"

[dependencies.rand]
version = "0.9"

[dependencies.rapidhash]
version = "4.1.0"

[dependencies.rayon]
version = "1"

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

[dependencies.serde_json]
version = "1.0"

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

[dependencies.thiserror]
version = "2.0"

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

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

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

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

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

[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"

[lints.clippy]
too_many_arguments = "allow"

[package]
authors = ["Bede Constantinides <b@bede.im>"]
autobenches = false
autobins = false
autoexamples = false
autolib = false
autotests = false
build = false
categories = ["science", "command-line-utilities"]
description = "Fast DNA search and [host] depletion using minimizers"
edition = "2024"
exclude = ["bench/*", "data/*"]
homepage = "https://github.com/bede/deacon"
keywords = ["bioinformatics", "genomics", "filtering", "decontamination"]
license = "MIT"
name = "deacon"
readme = "README.md"
repository = "https://github.com/bede/deacon"
version = "0.13.2"

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

[[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"