# THIS FILE IS AUTOMATICALLY GENERATED BY CARGO
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# to registry (e.g., crates.io) dependencies.
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# See Cargo.toml.orig for the original contents.

[package]
edition = "2024"
rust-version = "1.89"
name = "bismark-aligner"
version = "1.0.0"
authors = ["Felix Krueger"]
build = "build.rs"
autolib = false
autobins = false
autoexamples = false
autotests = false
autobenches = false
description = "Rust port of the Bismark Perl aligner wrapper (bismark)"
readme = "README.md"
keywords = [
    "bisulfite",
    "methylation",
    "bismark",
    "alignment",
    "bioinformatics",
]
categories = [
    "science::bioinformatics",
    "command-line-utilities",
]
license = "GPL-3.0-only"
repository = "https://github.com/FelixKrueger/Bismark"
resolver = "2"

[features]
binseq-input = ["dep:binseq"]
rammap-inprocess = [
    "dep:rammap-core",
    "dep:rayon",
]

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

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

[[test]]
name = "binseq_transcode"
path = "tests/binseq_transcode.rs"

[[test]]
name = "byte_identity_real_data"
path = "tests/byte_identity_real_data.rs"

[[test]]
name = "cli"
path = "tests/cli.rs"

[[test]]
name = "five_base_groundtruth"
path = "tests/five_base_groundtruth.rs"

[[test]]
name = "methylseq_conformance"
path = "tests/methylseq_conformance.rs"

[[test]]
name = "rammap_inprocess_crosscheck"
path = "tests/rammap_inprocess_crosscheck.rs"

[[test]]
name = "ubam_transcode"
path = "tests/ubam_transcode.rs"

[[test]]
name = "ubam_trimgalore_real"
path = "tests/ubam_trimgalore_real.rs"

[[bench]]
name = "parse_bench"
path = "benches/parse_bench.rs"
harness = false

[dependencies.anyhow]
version = "=1.0.103"

[dependencies.binseq]
version = "=0.9.2"
features = ["anyhow"]
optional = true
default-features = false

[dependencies.bismark-io]
version = "=1.0.0"

[dependencies.bismark-meta]
version = "1.0.0"

[dependencies.bstr]
version = "=1.10.0"

[dependencies.clap]
version = "=4.5.30"
features = ["derive"]

[dependencies.flate2]
version = "=1.1.9"

[dependencies.mimalloc]
version = "=0.1.52"
default-features = false

[dependencies.noodles-bam]
version = "=0.89.0"

[dependencies.noodles-bgzf]
version = "=0.47.0"

[dependencies.noodles-core]
version = "=0.20.0"

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

[dependencies.rammap-core]
version = "=1.1.1"
features = ["parallel"]
optional = true
default-features = false

[dependencies.rayon]
version = "1"
optional = true

[dependencies.thiserror]
version = "=2.0.18"

[dependencies.which]
version = "=7.0.3"

[dev-dependencies.assert_cmd]
version = "=2.0.16"

[dev-dependencies.criterion]
version = "=0.5.1"
features = ["cargo_bench_support"]
default-features = false

[dev-dependencies.predicates]
version = "=3.1.2"

[dev-dependencies.tempfile]
version = "=3.10.1"

[build-dependencies.bismark-meta]
version = "1.0.0"
