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Cargo.toml
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[package]
name = "alevin-fry"
version = "0.8.2"
authors = [
"Avi Srivastava <avi.srivastava@nyu.edu>",
"Hirak Sarkar <hirak_sarkar@hms.harvard.edu>",
"Dongze He <dhe17@umd.edu>",
"Mohsen Zakeri <mzakeri@cs.umd.edu>",
"Rob Patro <rob@cs.umd.edu>",
]
edition = "2021"
description = "A suite of tools for the rapid, accurate and memory-frugal processing single-cell and single-nucleus sequencing data."
license-file = "LICENSE"
readme = "README.md"
repository = "https://github.com/COMBINE-lab/alevin-fry"
homepage = "https://github.com/COMBINE-lab/alevin-fry"
documentation = "https://alevin-fry.readthedocs.io/en/latest/"
include = [
"/src/*.rs",
"/Cargo.toml",
"/README.md",
"/LICENSE",
"/CONTRIBUTING.md",
"/CODE_OF_CONDUCT.md",
]
keywords = [
"single-cell",
"preprocessing",
"RNA-seq",
"single-nucleus",
"RNA-velocity",
]
categories = ["command-line-utilities", "science"]
[workspace]
[dependencies]
# for local development, look in the libradicl git repository
# but when published, pull the specified version
libradicl = { git = "https://github.com/COMBINE-lab/libradicl", branch = "develop", version = "0.6.0" }
anyhow = "1.0.71"
arrayvec = "0.7.4"
ahash = "0.8.3"
bincode = "1.3.3"
bstr = "1.5.0"
crossbeam-channel = "0.5.8"
crossbeam-queue = "0.3.8"
# derive_builder = "0.11.2"
typed-builder = "0.14.0"
indicatif = "0.17.5"
needletail = "0.5.1"
petgraph = "0.6.3"
flate2 = "1.0.26"
scroll = "0.11.0"
serde = { version = "1.0.164", features = ["derive"] }
serde_json = "1.0.99"
sprs = "0.11.1"
slog = "2.7.0"
slog-term = "2.9.0"
slog-async = "2.7.0"
smallvec = "1.10.0"
snap = "1.1.0"
rand = "0.8.5"
chrono = "0.4.26"
csv = "1.2.2"
mimalloc = { version = "0.1.37", default-features = false }
num-format = "0.4.4"
num_cpus = "1.16.0"
bio-types = { version = "1.0.0", default-features = true, features = ["serde"] }
itertools = "0.11.0"
thiserror = "1.0.40"
statrs = "0.16.0"
rust-htslib = { version = "0.44.1", default-features = false, features = [
"bzip2",
"lzma",
] }
sce = { git = "https://github.com/parazodiac/SingleCellExperiment", branch = "dev", version = "0.2.0" }
# no shenanigans; clap makes breaking "fixes" too often to allow variability
# in the version different from what we tested with
clap = { version = "=4.3.9", features = ["derive", "wrap_help", "cargo", "help", "usage", "string", "error-context"] }
[profile.release]
#debug = true
lto = "thin"
#codegen-units=1
opt-level = 3