chaintools 0.0.13

work with .chain files in Rust
Documentation 
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[package]
name = "chaintools"
version = "0.0.13"
edition = "2024"
authors = ["alejandrogzi <alejandrxgzi@gmail.com>"]
license = "MIT"
description = "work with .chain files in Rust"
homepage = "https://github.com/alejandrogzi/chaintools"
repository = "https://github.com/alejandrogzi/chaintools"
readme = "README.md"
keywords = ["chain", "lib", "genomic", "tool"]
default-run = "chaintools"

[features]
default = ["mmap"]
cli = ["dep:clap", "dep:genepred", "dep:log", "dep:simple_logger", "sequence", "write", "dep:num_cpus", "dep:rust-lapper", "parallel"]
mmap = ["memmap2"]
gzip = ["dep:flate2", "flate2/zlib-rs", "genepred?/gzip"]
parallel = ["rayon"]
index = []
write = []
sequence = ["dep:twobit"]
# BAM output for `convert --to bam`. Optional so library and non-BAM CLI builds
# do not pull the BAM writer; VCF and MAF conversion never touch it.
bam = ["dep:noodles-bam", "dep:noodles-core", "dep:noodles-sam"]

[dependencies]
clap = { version = "4", features = ["derive"], optional = true }
flate2 = { version = "1", optional = true, default-features = false }
genepred = { version = "0.0.16", optional = true }
memchr = "2"
memmap2 = { version = "0.9", optional = true }
noodles-bam = { version = "0.94", optional = true }
noodles-core = { version = "0.20", optional = true }
noodles-sam = { version = "0.89", optional = true }
rayon = { version = "1", optional = true }
rust-lapper = { version = "1", optional = true }
log = { version = "0.4.29", optional = true }
simple_logger = { version = "5.2.0", optional = true, features = ["stderr"] }
twobit = { version = "0.2.2", optional = true }
num_cpus = { version = "1.17.0", optional = true }

[[bin]]
name = "chaintools"
path = "src/main.rs"
required-features = ["cli"]

[[bin]]
name = "benchmark"
path = "bench/benchmark.rs"
required-features = ["cli"]

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