mehari 0.41.0

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[package]
edition = "2021"
rust-version = "1.75.0"
name = "mehari"
version = "0.41.0"
authors = ["Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>"]
build = "build.rs"
autolib = false
autobins = false
autoexamples = false
autotests = false
autobenches = false
description = "Variant effect prediction all in Rust"
readme = "README.md"
license = "MIT"
repository = "https://github.com/varfish-org/mehari"
resolver = "3"

[package.metadata.docs.rs]
all-features = true

[features]
default = ["jemalloc"]
dhat-heap = ["dep:dhat"]
documentation = []
jemalloc = [
    "dep:tikv-jemallocator",
    "rocksdb/jemalloc",
    "annonars/jemalloc",
]

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

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

[dependencies.actix-web]
version = "4.12"

[dependencies.annonars]
version = "0.44.1"
default-features = false

[dependencies.anyhow]
version = "1.0"

[dependencies.async-compression]
version = "0.4"
features = [
    "tokio",
    "gzip",
]

[dependencies.bio]
version = "3.0.0"

[dependencies.biocommons-bioutils]
version = "0.1.5"

[dependencies.built]
version = "0.8"
features = [
    "chrono",
    "semver",
]

[dependencies.byte-unit]
version = "5.2"

[dependencies.chrono]
version = "0.4"

[dependencies.clap]
version = "4.6"
features = ["derive"]

[dependencies.clap-verbosity-flag]
version = "3.0"

[dependencies.csv]
version = "1.4"

[dependencies.derivative]
version = "2.2"

[dependencies.derive-new]
version = "0.7.0"

[dependencies.derive_builder]
version = "0.20"
features = ["clippy"]

[dependencies.dhat]
version = "0.3.3"
optional = true

[dependencies.enumflags2]
version = "0.7.11"
features = ["serde"]

[dependencies.env_logger]
version = "0.11"

[dependencies.flate2]
version = "1.1"

[dependencies.futures]
version = "0.3"

[dependencies.hgvs]
version = "0.20.1"

[dependencies.indexmap]
version = "2.13"
features = ["serde"]

[dependencies.itertools]
version = "0.14"

[dependencies.jsonl]
version = "4.0"

[dependencies.log]
version = "0.4"

[dependencies.memmap2]
version = "0.9.10"

[dependencies.nom]
version = "8.0"

[dependencies.noodles]
version = "0.97.0"
features = [
    "async",
    "bgzf",
    "core",
    "vcf",
    "bcf",
    "csi",
    "fasta",
    "tabix",
]

[dependencies.nutype]
version = "0.6.2"
features = ["serde"]

[dependencies.once_cell]
version = "1.21.4"

[dependencies.parse-display]
version = "0.10"

[dependencies.pbjson]
version = "0.9"

[dependencies.percent-encoding]
version = "2.3"

[dependencies.procfs]
version = "0.18"

[dependencies.prost]
version = "0.14.3"

[dependencies.quick_cache]
version = "0.6.18"

[dependencies.rand]
version = "0.10"

[dependencies.rayon]
version = "1.11.0"

[dependencies.rocksdb]
version = "0.24.0"
features = ["multi-threaded-cf"]

[dependencies.rustc-hash]
version = "2.1.0"

[dependencies.seqrepo]
version = "0.10.2"
features = ["cached"]

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

[dependencies.serde-aux]
version = "4.7.0"

[dependencies.serde_json]
version = "1.0"

[dependencies.serde_with]
version = "3.16"
features = [
    "alloc",
    "macros",
    "indexmap_2",
]
default-features = false

[dependencies.serde_yaml]
version = "0.9"

[dependencies.strum]
version = "0.28"
features = ["derive"]

[dependencies.tempfile]
version = "3"

[dependencies.thousands]
version = "0.2"

[dependencies.tokio]
version = "1.50"
features = [
    "rt-multi-thread",
    "macros",
]

[dependencies.tracing]
version = "0.1"
features = ["log"]

[dependencies.tracing-subscriber]
version = "0.3"

[dependencies.utoipa]
version = "5.4.0"
features = [
    "actix_extras",
    "chrono",
    "indexmap",
    "openapi_extensions",
    "preserve_order",
    "yaml",
]

[dependencies.utoipa-swagger-ui]
version = "9.0.2"
features = ["actix-web"]

[dependencies.uuid]
version = "1.22"
features = [
    "fast-rng",
    "serde",
]

[dependencies.zstd]
version = "0.13"

[dev-dependencies.criterion]
version = "0.8.2"
features = ["async_tokio"]

[dev-dependencies.csv]
version = "1.4"

[dev-dependencies.hxdmp]
version = "0.2"

[dev-dependencies.insta]
version = "1.46"
features = ["yaml"]

[dev-dependencies.pprof]
version = "0.15.0"
features = ["flamegraph"]

[dev-dependencies.pretty_assertions]
version = "1.4"

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

[dev-dependencies.temp_testdir]
version = "0.2"

[dev-dependencies.tracing-test]
version = "0.2"

[build-dependencies.anyhow]
version = "1.0"

[build-dependencies.built]
version = "0.8"
features = [
    "cargo-lock",
    "dependency-tree",
    "git2",
    "chrono",
    "semver",
]

[build-dependencies.pbjson-build]
version = "0.9.0"

[build-dependencies.prost-build]
version = "0.14.3"

[target.'cfg(not(target_env = "msvc"))'.dependencies.tikv-jemallocator]
version = "0.6"
optional = true