# THIS FILE IS AUTOMATICALLY GENERATED BY CARGO
#
# When uploading crates to the registry Cargo will automatically
# "normalize" Cargo.toml files for maximal compatibility
# with all versions of Cargo and also rewrite `path` dependencies
# to registry (e.g., crates.io) dependencies.
#
# If you are reading this file be aware that the original Cargo.toml
# will likely look very different (and much more reasonable).
# See Cargo.toml.orig for the original contents.

[package]
edition = "2021"
name = "lorikeet-genome"
version = "0.8.2"
authors = ["Rhys Newell <rhys.newell94@gmail.com>"]
include = [
    "/src",
    "/LICENSE",
    "/README.md",
    "/Cargo.toml",
]
default-run = "lorikeet"
description = "Strain resolver and variant caller via local reassembly for metagenomics"
homepage = "https://rhysnewell.github.io/Lorikeet/"
documentation = "https://github.com/rhysnewell/Lorikeet"
readme = "README.md"
keywords = [
    "bioinformatics",
    "metagenomics",
    "variant-calling",
    "strain-anlaysis",
]
categories = [
    "bioinformatics::metagenomics",
    "bioinformatics::variant-calling",
    "bioinformatics::strain-analysis",
]
license = "GPL-3.0"
repository = "https://github.com/rhysnewell/Lorikeet"

[profile.bench]
opt-level = 3
lto = true
codegen-units = 16
debug = 0
debug-assertions = false
rpath = false
panic = "unwind"
overflow-checks = false
incremental = false

[profile.dev]
opt-level = 0
lto = true
codegen-units = 16
debug = 2
debug-assertions = true
rpath = false
panic = "unwind"
overflow-checks = true
incremental = true

[profile.release]
opt-level = 3
lto = true
codegen-units = 16
debug = 0
debug-assertions = false
rpath = false
panic = "unwind"
overflow-checks = false
incremental = false
strip = true

[profile.test]
opt-level = 3
lto = true
codegen-units = 16
debug = 2
debug-assertions = true
rpath = false
panic = "unwind"
overflow-checks = true
incremental = true

[lib]
bench = false

[dependencies.ansi_term]
version = "^0.12"

[dependencies.anyhow]
version = "1.0.70"

[dependencies.approx]
version = "^0.5"

[dependencies.bio]
version = "^1.1"

[dependencies.bio-types]
version = "^1.0"

[dependencies.bird_tool_utils]
version = "^0.4"

[dependencies.bird_tool_utils-man]
version = "^0.4"

[dependencies.bstr]
version = "^0.2.17"

[dependencies.clap]
version = "^4"
features = ["cargo"]

[dependencies.clap_complete]
version = "^4"

[dependencies.compare]
version = "^0.1"

[dependencies.enum-ordinalize]
version = "^3.1"

[dependencies.env_logger]
version = "^0.6"

[dependencies.gkl]
version = "^0.1.1"

[dependencies.glob]
version = "^0.3"

[dependencies.hashlink]
version = "^0.7"

[dependencies.indexmap]
version = "^1.7"

[dependencies.indicatif]
version = "^0.17"

[dependencies.itertools]
version = "^0.8"

[dependencies.lazy_static]
version = "^1.3"

[dependencies.libm]
version = "^0.2"

[dependencies.log]
version = "^0.4"

[dependencies.mathru]
version = "^0.14"

[dependencies.multimap]
version = "^0.9"

[dependencies.ndarray]
version = "^0.15"
features = ["rayon"]

[dependencies.ndarray-npy]
version = "^0.8"

[dependencies.needletail]
version = "^0.5"

[dependencies.nix]
version = "0.26.2"

[dependencies.num]
version = "0.4.0"

[dependencies.ordered-float]
version = "1"

[dependencies.partitions]
version = "^0.2"

[dependencies.petgraph]
version = "^0.6"
features = ["stable_graph"]

[dependencies.pyo3]
version = "^0.17"
optional = true

[dependencies.rand]
version = "0.6"

[dependencies.rayon]
version = "^1.5.1"

[dependencies.roff]
version = "^0.2"

[dependencies.rust-htslib]
version = "^0.44"
default-features = false

[dependencies.scoped_threadpool]
version = "^0.1.9"

[dependencies.serde]
version = "^1"

[dependencies.serde_derive]
version = "^1"

[dependencies.statrs]
version = "^0.16"

[dependencies.strum]
version = "^0.17"

[dependencies.strum_macros]
version = "^0.17"

[dependencies.tempdir]
version = "^0.3"

[dependencies.tempfile]
version = "^3"

[dependencies.term]
version = "^0.7"

[dev-dependencies.assert_cli]
version = "0.6.*"

[features]
bam = []
default = [
    "fst",
    "bam",
]
fst = ["dep:pyo3"]