omicsx 1.0.2

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[package]
edition = "2021"
name = "omicsx"
version = "1.0.2"
authors = ["Raghav Maheshwari <raghavmkota@gmail.com>"]
build = "build.rs"
autolib = false
autobins = false
autoexamples = false
autotests = false
autobenches = false
description = "omicsx: SIMD-accelerated sequence alignment and bioinformatics analysis for petabyte-scale genomic data"
homepage = "https://github.com/techusic/omicsx"
documentation = "https://docs.rs/omicsx"
readme = "README.md"
keywords = [
    "bioinformatics",
    "simd",
    "alignment",
    "genomics",
    "cuda",
]
categories = [
    "algorithms",
    "data-structures",
    "science",
]
license = "Apache-2.0 OR MIT"
repository = "https://github.com/techusic/omicsx"

[features]
all-gpu = [
    "cuda",
    "hip",
    "vulkan",
]
cuda = [
    "cudarc",
    "cuda-13100",
]
cuda-11040 = []
cuda-11050 = []
cuda-11060 = []
cuda-11070 = []
cuda-11080 = []
cuda-12000 = []
cuda-12010 = []
cuda-12020 = []
cuda-12030 = []
cuda-12040 = []
cuda-12050 = []
cuda-13000 = []
cuda-13010 = []
cuda-13100 = []
cuda-full = ["cuda"]
default = ["simd"]
hip = []
simd = []
vulkan = []

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

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

[[example]]
name = "bam_format"
path = "examples/bam_format.rs"

[[example]]
name = "basic_alignment"
path = "examples/basic_alignment.rs"

[[example]]
name = "distributed_alignment"
path = "examples/distributed_alignment.rs"

[[example]]
name = "gpu_acceleration"
path = "examples/gpu_acceleration.rs"

[[example]]
name = "gpu_execution_test"
path = "examples/gpu_execution_test.rs"

[[example]]
name = "multiformat_hmm_parser"
path = "examples/multiformat_hmm_parser.rs"

[[example]]
name = "neon_alignment"
path = "examples/neon_alignment.rs"

[[example]]
name = "performance_validation"
path = "examples/performance_validation.rs"

[[example]]
name = "sam_format_output"
path = "examples/sam_format_output.rs"

[[example]]
name = "st_jude_integration"
path = "examples/st_jude_integration.rs"

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

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

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

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

[[bench]]
name = "gpu_benchmarks"
path = "benches/gpu_benchmarks.rs"

[dependencies.bincode]
version = "1.3"

[dependencies.criterion]
version = "0.5"
features = ["html_reports"]

[dependencies.cudarc]
version = "0.12"
features = ["std"]
optional = true

[dependencies.flate2]
version = "1.0"

[dependencies.log]
version = "0.4"

[dependencies.rayon]
version = "1.7"

[dependencies.regex]
version = "1.12.3"

[dependencies.serde]
version = "1.0"
features = ["derive"]

[dependencies.serde_json]
version = "1.0"

[dependencies.thiserror]
version = "1.0"

[dev-dependencies.criterion]
version = "0.5"
features = ["html_reports"]

[dev-dependencies.rand]
version = "0.8"

[profile.bench]
opt-level = 3
lto = true
codegen-units = 1

[profile.release]
opt-level = 3
lto = true
codegen-units = 1