# 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 = "2024"
rust-version = "1.95"
name = "kira-ls-aligner"
version = "0.3.0"
build = "build.rs"
autolib = false
autobins = false
autoexamples = false
autotests = false
autobenches = false
description = "Unified short- and long-read sequence aligner written in Rust 2024. It combines minimap2-style minimizers and chaining with BWA-MEM2-style exact-match anchoring and output semantics. The goal is drop-in compatibility with bwa-mem pipelines while supporting long reads efficiently."
readme = "README.md"
keywords = [
    "bioinformatics",
    "genomics",
    "sequence-alignment",
    "dna",
    "sam",
]
categories = [
    "science",
    "science::bioinformatics",
    "science::bioinformatics::sequence-analysis",
    "command-line-utilities",
    "algorithms",
]
license = "MIT"
repository = "https://github.com/ARyaskov/kira-ls-aligner"

[features]
cuda = [
    "dep:cudarc",
    "dep:find_cuda_helper",
]
default = []

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

[[bin]]
name = "kira_ls_aligner"
path = "src/bin/kira_ls_aligner.rs"

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

[[test]]
name = "splice_e2e"
path = "tests/splice_e2e.rs"

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

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

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

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

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

[dependencies.aho-corasick]
version = "1.1"

[dependencies.anyhow]
version = "1"

[dependencies.clap]
version = "4"
features = ["derive"]

[dependencies.core_affinity]
version = "0.8"

[dependencies.cudarc]
version = "0.16"
features = [
    "std",
    "driver",
    "cuda-12060",
    "dynamic-loading",
]
optional = true
default-features = false

[dependencies.indicatif]
version = "0.18"

[dependencies.kira-bam]
version = "0.1.2"

[dependencies.kira-fastq]
version = "0.3.0"

[dependencies.kira-simd]
version = "0.1.0"
features = [
    "runtime-dispatch",
    "avx2",
    "sse42",
    "neon",
    "scalar",
]

[dependencies.kira_kv_engine]
version = "0.6.1"
default-features = true

[dependencies.memmap2]
version = "0.9"

[dependencies.needletail]
version = "0.6"

[dependencies.rayon]
version = "1.10"

[dependencies.rustc-hash]
version = "2"

[dependencies.sysinfo]
version = "0.38"

[dependencies.tempfile]
version = "3"

[dependencies.thiserror]
version = "2"

[dev-dependencies.criterion]
version = "0.5"
features = ["cargo_bench_support"]
default-features = false

[build-dependencies.find_cuda_helper]
version = "0.2"
optional = true

[target."cfg(windows)".dependencies.windows-sys]
version = "0.59"
features = [
    "Win32_System_SystemInformation",
    "Win32_Foundation",
]

[profile.release]
lto = "thin"
codegen-units = 1
strip = "debuginfo"
