# 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 = "alevin-fry"
version = "0.11.0"
authors = [
    "Avi Srivastava <asrivastava@wistar.org>",
    "Hirak Sarkar <hiraksarkar.cs@gmail.com>",
    "Dongze He <dhe17@umd.edu>.zakeri@gmail.com>",
    "Noor Pratap Singh <npsingh@umd.edu>",
    "Rob Patro <rob@cs.umd.edu>",
]
build = false
include = [
    "/src/*.rs",
    "/src/atac/*.rs",
    "/Cargo.toml",
    "/README.md",
    "/LICENSE",
    "/CONTRIBUTING.md",
    "/CODE_OF_CONDUCT.md",
]
autobins = false
autoexamples = false
autotests = false
autobenches = false
description = "A suite of tools for the rapid, accurate and memory-frugal processing single-cell and single-nucleus sequencing data."
homepage = "https://github.com/COMBINE-lab/alevin-fry"
documentation = "https://alevin-fry.readthedocs.io/en/latest/"
readme = "README.md"
keywords = [
    "single-cell",
    "preprocessing",
    "RNA-seq",
    "ATAC-seq",
    "single-nucleus",
]
categories = [
    "command-line-utilities",
    "science",
]
license-file = "LICENSE"
repository = "https://github.com/COMBINE-lab/alevin-fry"

[profile.dist]
lto = "thin"
inherits = "release"

[profile.release]
opt-level = 3
lto = "thin"

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

[[bin]]
name = "alevin-fry"
path = "src/main.rs"

[dependencies.ahash]
version = "0.8.11"

[dependencies.anyhow]
version = "1.0.86"

[dependencies.arrayvec]
version = "0.7.4"

[dependencies.bincode]
version = "1.3.3"

[dependencies.bio-types]
version = "1.0.2"
features = ["serde"]
default-features = true

[dependencies.bstr]
version = "1.9.1"

[dependencies.chrono]
version = "0.4.38"

[dependencies.clap]
version = "4.5.23"
features = [
    "derive",
    "wrap_help",
    "cargo",
    "help",
    "usage",
    "string",
    "error-context",
]

[dependencies.crossbeam-channel]
version = "0.5.13"

[dependencies.crossbeam-queue]
version = "0.3.11"

[dependencies.csv]
version = "1.3.0"

[dependencies.dashmap]
version = "6.1.0"
features = [
    "serde",
    "inline",
]

[dependencies.flate2]
version = "1.0.30"

[dependencies.indicatif]
version = "0.17.8"

[dependencies.itertools]
version = "0.13.0"

[dependencies.libradicl]
version = "0.10.0"

[dependencies.mimalloc]
version = "0.1.43"
default-features = false

[dependencies.nalgebra]
version = "0.33.2"

[dependencies.needletail]
version = "0.6.0"

[dependencies.noodles]
version = "0.85.0"
features = [
    "bam",
    "bgzf",
    "sam",
]

[dependencies.num-format]
version = "0.4.4"

[dependencies.num_cpus]
version = "1.16.0"

[dependencies.petgraph]
version = "0.6.5"

[dependencies.rand]
version = "0.8.5"

[dependencies.sce]
version = "0.2.0"

[dependencies.scroll]
version = "0.12.0"

[dependencies.serde]
version = "1.0.204"
features = ["derive"]

[dependencies.serde_json]
version = "1.0.120"

[dependencies.slog]
version = "2.7.0"

[dependencies.slog-async]
version = "2.8.0"

[dependencies.slog-term]
version = "2.9.1"

[dependencies.smallvec]
version = "1.13.2"

[dependencies.snap]
version = "1.1.1"

[dependencies.sprs]
version = "0.11.1"

[dependencies.statrs]
version = "0.18.0"

[dependencies.thiserror]
version = "2.0.4"

[dependencies.typed-builder]
version = "0.20.0"