oarfish 0.10.0

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# See Cargo.toml.orig for the original contents.

[package]
edition = "2024"
rust-version = "1.91"
name = "oarfish"
version = "0.10.0"
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",
    "/CHANGELOG.md",
    "/LICENSE",
]
autolib = false
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"

[features]
default = ["mimalloc"]
mimalloc = ["dep:mimalloc"]

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

[dependencies.anyhow]
version = "1.0.100"

[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.bramble-rs]
version = "0.1.4"

[dependencies.bstr]
version = "1.12.1"

[dependencies.clap]
version = "4.5.57"
features = ["derive"]

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

[dependencies.csv]
version = "1.4"

[dependencies.either]
version = "1.15.0"

[dependencies.humantime]
version = "2.3.0"

[dependencies.indicatif]
version = "0.18.3"

[dependencies.itertools]
version = "0.14.0"

[dependencies.kders]
version = "0.1.1"

[dependencies.lz4]
version = "1.28.1"

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

[dependencies.needletail]
version = "0.6.3"

[dependencies.niffler]
version = "3.0.0"

[dependencies.noodles-bam]
version = "0.87.0"

[dependencies.noodles-bgzf]
version = "0.46.0"

[dependencies.noodles-sam]
version = "0.83.0"

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

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

[dependencies.rammap]
version = "1.2.0"
features = ["parallel"]
default-features = false
package = "rammap-core-temp"

[dependencies.rand]
version = "0.10.0"

[dependencies.rayon]
version = "1.11"

[dependencies.rustc-hash]
version = "2.1.1"

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

[dependencies.seqcol_rs]
version = "0.4.1"

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

[dependencies.serde_json]
version = "1.0.149"

[dependencies.sprs]
version = "0.11.4"

[dependencies.statrs]
version = "0.18"

[dependencies.tabled]
version = "0.20.0"

[dependencies.tracing]
version = "0.1.44"

[dependencies.tracing-subscriber]
version = "0.3.22"
features = ["env-filter"]

[dependencies.typed-builder]
version = "0.23.2"

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

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