[package]
authors = ["Johannes Köster <johannes.koester@tu-dortmund.de>", "David Lähnemann <david.laehnemann@uni-duesseldorf.de>"]
description = "A library for calling of genomic variants using a latent variable model."
edition = "2018"
include = ["src/**/*", "Cargo.toml", "CHANGELOG.md", "README.md", "LICENSE", "templates/*"]
license = "GPL-3.0"
name = "varlociraptor"
readme = "README.md"
repository = "https://github.com/varlociraptor/varlociraptor"
version = "8.4.11"

[dependencies]
GSL = "6.0"
anyhow = "1.0"
approx = "0.5.0"
askama = "0.11.1"
auto_ops = "0.3.0"
bincode = "1.3"
bio = "2.0.0"
bio-types = { version = ">=0.12", features = ["serde"] }
boolean_expression = "0.4"
bv = "0.11"
byteorder = "1.3"
cached = "0.42"
clap = { version = "2", features = ["yaml", "color", "suggestions"] }
counter = "0.5"
csv = "1"
data-encoding = "2.3"
derefable = "0.1"
derive-new = "0.5"
derive_builder = "0.12.0"
eval = "0.4"
fern = "0.6"
getset = "0.1.0"
half = { version = "2.3", features = ["serde"] }
itertools = "0.10"
itertools-num = "0.1"
jemallocator = "0.5.0"
lazy_static = "1"
log = "0.4"
lru = "0.7"
lru_time_cache = "0.11"
ndarray = { version = "0.15", features = ["serde"] }
num-traits = "0.2"
ordered-float = { version = "1", features = ["serde"] }
paste = "1"
pest = "2"
pest_derive = "2"
petgraph = "0.6"
progress-logger = "0.3"
rand = "0.8"
rayon = "1"
regex = "1"
ring = "0.16"
rust-htslib = "0.47.0"
rusty-machine = "0.5"
serde = "1"
serde_derive = "1"
serde_json = "1"
serde_yaml = ">=0.8.4,<0.9"
shrinkwraprs = "0.3.0"
statrs = "0.16"
structopt = "0.3"
strum = ">= 0.16, < 0.26" # Needs to be in sync with rust-bios strum dependency
strum_macros = ">= 0.16, < 0.26"
tempfile = "3"
thiserror = "1.0"
time = "0.3"
typed-builder = "0.12"
uuid = { version = "0.8", features = ["v4"] }
vec_map = "0.8"
yaml-rust = ">=0.4.1,<0.5"
linear-map = "1.2"

[dev-dependencies]
env_logger = "0.9.0"
serde_json = "1"

[features]
default = []
use-intrinsics = ["half/use-intrinsics"]

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

[profile.develop]
codegen-units = 128
inherits = "release"
lto = false