# 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 = "oarfish"
version = "0.6.5"
authors = [
    "Zahra Zare Jousheghani <zzare@umd.edu>",
    "Noor Pratap Singh <npsingh@umd.edu>",
    "Rob Patro <rob@cs.umd.edu>",
]
build = false
include = [
    "/src/*.rs",
    "/src/util/*.rs",
    "/Cargo.toml",
    "/Cargo.lock",
    "/README.md",
    "/LICENSE",
]
autobins = false
autoexamples = false
autotests = false
autobenches = false
description = "A fast, accurate and versatile tool for long-read transcript quantification."
homepage = "https://COMBINE-lab.github.io/oarfish"
readme = "README.md"
keywords = [
    "RNA-seq",
    "quantification",
    "long-read",
    "transcriptomics",
]
categories = [
    "command-line-utilities",
    "science",
]
license-file = "LICENSE"
repository = "https://github.com/COMBINE-lab/oarfish"

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

[profile.release]
lto = "thin"
debug-assertions = false
panic = "abort"

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

[dependencies.anyhow]
version = "1.0.93"

[dependencies.arrow2]
version = "0.18.0"
features = [
    "io_parquet",
    "io_parquet_gzip",
    "io_parquet_zstd",
    "io_parquet_snappy",
]

[dependencies.atomic_float]
version = "1.1.0"

[dependencies.bio-types]
version = "1.0.4"
features = ["serde"]

[dependencies.bstr]
version = "1.11.0"

[dependencies.clap]
version = "4.5.21"
features = ["derive"]

[dependencies.crossbeam]
version = "0.8.4"
features = [
    "crossbeam-queue",
    "crossbeam-channel",
]

[dependencies.csv]
version = "1.3"

[dependencies.either]
version = "1.13.0"

[dependencies.indicatif]
version = "0.17.9"

[dependencies.itertools]
version = "0.13.0"

[dependencies.kders]
version = "0.1.1"

[dependencies.lz4]
version = "1.28.0"

[dependencies.minimap2]
version = "0.1.21"

[dependencies.minimap2-sys]
version = "0.1.20"

[dependencies.needletail]
version = "0.6.0"

[dependencies.noodles-bam]
version = "0.70.0"

[dependencies.noodles-bgzf]
version = "0.33.0"

[dependencies.noodles-sam]
version = "0.66.0"

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

[dependencies.path-tools]
version = "0.1.0"

[dependencies.rand]
version = "0.8.5"

[dependencies.rayon]
version = "1.10"

[dependencies.rustc-hash]
version = "2.0.0"

[dependencies.sendable-swapvec]
version = "0.4.3"

[dependencies.seqcol_rs]
version = "0.1.3"

[dependencies.serde]
version = "1"
features = ["derive"]

[dependencies.serde_json]
version = "1.0.133"

[dependencies.sprs]
version = "0.11.2"

[dependencies.statrs]
version = "0.17"

[dependencies.tabled]
version = "0.17.0"

[dependencies.tracing]
version = "0.1.41"

[dependencies.tracing-subscriber]
version = "0.3.18"
features = ["env-filter"]

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