fibertools-rs 0.8.2

# THIS FILE IS AUTOMATICALLY GENERATED BY CARGO
#
# When uploading crates to the registry Cargo will automatically
# "normalize" Cargo.toml files for maximal compatibility
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# to registry (e.g., crates.io) dependencies.
#
# If you are reading this file be aware that the original Cargo.toml
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# See Cargo.toml.orig for the original contents.

[package]
edition = "2021"
name = "fibertools-rs"
version = "0.8.2"
authors = ["Mitchell R. Vollger <mrvollger@gmail.com>"]
build = "build.rs"
exclude = [
    "py-ft/",
    "tests/data/",
]
autolib = false
autobins = false
autoexamples = false
autotests = false
autobenches = false
description = "Fiber-seq toolkit in rust"
homepage = "https://fiberseq.github.io/"
readme = "README.md"
keywords = [
    "cli",
    "bam",
    "bfx",
]
categories = ["command-line-utilities"]
license = "MIT"
repository = "https://github.com/fiberseq/fibertools-rs"

[features]
burn = ["dep:burn"]
cli = [
    "dep:clap",
    "dep:clap_complete",
    "dep:clap_mangen",
    "dep:console",
]
default = [
    "cli",
    "burn",
]
tch = [
    "dep:tch",
    "burn/tch",
]

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

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

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

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

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

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

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

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

[[test]]
name = "m6a_prediction_test"
path = "tests/m6a_prediction_test.rs"

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

[dependencies.anstyle]
version = "1.0.0"

[dependencies.anyhow]
version = "1.0.58"

[dependencies.bio]
version = "1.2.0"

[dependencies.burn]
version = "0.18.0"
features = ["candle"]
optional = true

[dependencies.clap]
version = "4.4.6"
features = [
    "cargo",
    "string",
    "wrap_help",
    "color",
    "unstable-styles",
    "derive",
    "env",
]
optional = true

[dependencies.clap_complete]
version = "4.0.6"
optional = true

[dependencies.clap_mangen]
version = "0.2.5"
optional = true

[dependencies.colored]
version = "2.0.0"

[dependencies.console]
version = "0.15"
optional = true

[dependencies.derive_builder]
version = "0.12.0"

[dependencies.duct]
version = "1.1.0"

[dependencies.env_logger]
version = "0.9.0"

[dependencies.gbdt]
version = "=0.1.3"

[dependencies.gzp]
version = "0.11.3"

[dependencies.indicatif]
version = "0.17.7"
features = ["rayon"]

[dependencies.itertools]
version = "0.10.5"

[dependencies.lazy_static]
version = "1.4.0"

[dependencies.linear-map]
version = "1.2.0"

[dependencies.log]
version = "0.4"

[dependencies.niffler]
version = "2.5.0"
features = ["gz"]
default-features = false

[dependencies.noodles]
version = "0.100.0"
features = [
    "fasta",
    "bed",
]

[dependencies.num]
version = "0.4.3"

[dependencies.ordered-float]
version = "3.4.0"

[dependencies.polars]
version = "0.51.0"
features = [
    "csv",
    "decompress",
    "lazy",
]

[dependencies.rand]
version = "0.8.5"

[dependencies.rayon]
version = "1.10"

[dependencies.regex]
version = "1.9.1"

[dependencies.rust-htslib]
version = "0.46"

[dependencies.rust-lapper]
version = "1.2.0"

[dependencies.serde]
version = "1.0.104"
features = ["derive"]
optional = false

[dependencies.serde_json]
version = "1.0.48"
optional = false

[dependencies.serde_yaml]
version = "0.9"

[dependencies.spin]
version = "0.9.8"

[dependencies.tch]
version = "0.19.0"
optional = true

[dependencies.tempfile]
version = "3.3.0"

[dev-dependencies.assert_cmd]
version = "2.0.11"

[dev-dependencies.predicates]
version = "3.0.3"

[build-dependencies.burn-import]
version = "0.18.0"
features = ["onnx"]
default-features = false

[build-dependencies.vergen-git2]
version = "1.0.2"
features = [
    "build",
    "cargo",
    "rustc",
    "si",
]

[profile.dev]
opt-level = 0
debug = 0

[profile.dist]
split-debuginfo = "packed"
inherits = "release"

[profile.release]
lto = true
codegen-units = 1
debug = 0
panic = "abort"
strip = "debuginfo"

[profile.test]
opt-level = 2
lto = false
codegen-units = 256
incremental = true
inherits = "dev"
strip = "none"