oarfish 0.9.2

A fast, accurate and versatile tool for long-read transcript quantification.
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[[bin]]
name = "oarfish"
path = "src/main.rs"

[dependencies.anyhow]
version = "1.0.100"

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

[dependencies.atomic_float]
version = "1.1.0"

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

[dependencies.bstr]
version = "1.12.1"

[dependencies.clap]
features = ["derive"]
version = "4.5.54"

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

[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.minimap2]
version = "0.1.28"

[dependencies.minimap2-sys]
version = "0.1.24"

[dependencies.needletail]
version = "0.6.3"

[dependencies.niffler]
version = "3.0.0"

[dependencies.noodles-bam]
version = "0.85.0"

[dependencies.noodles-bgzf]
version = "0.45.0"

[dependencies.noodles-sam]
version = "0.81.0"

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

[dependencies.parse-size]
version = "1.1.0"

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

[dependencies.rand]
version = "0.9.2"

[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]
features = ["derive"]
version = "1"

[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]
features = ["env-filter"]
version = "0.3.22"

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

[package]
authors = ["Zahra Zare Jousheghani <zzare@umd.edu>", "Noor Pratap Singh <npsingh@umd.edu>", "Rob Patro <rob@cs.umd.edu>"]
autobenches = false
autobins = false
autoexamples = false
autolib = false
autotests = false
build = false
categories = ["command-line-utilities", "science"]
description = "A fast, accurate and versatile tool for long-read transcript quantification."
edition = "2024"
homepage = "https://COMBINE-lab.github.io/oarfish"
include = ["/src/*.rs", "/src/util/*.rs", "/Cargo.toml", "/Cargo.lock", "/README.md", "/LICENSE"]
keywords = ["RNA-seq", "quantification", "long-read", "transcriptomics"]
license-file = "LICENSE"
name = "oarfish"
readme = "README.md"
repository = "https://github.com/COMBINE-lab/oarfish"
rust-version = "1.91"
version = "0.9.2"

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

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