varforge 0.1.0

Synthetic cancer sequencing test data generator
Documentation 
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[package]
name = "varforge"
version = "0.1.0"
edition = "2021"
rust-version = "1.74"
description = "Synthetic cancer sequencing test data generator"
repository = "https://github.com/trentzz/varforge"
homepage = "https://github.com/trentzz/varforge"
documentation = "https://docs.rs/varforge"
license = "MIT"
readme = "README.md"
keywords = ["bioinformatics", "sequencing", "cancer", "simulation", "genomics"]
categories = ["science", "command-line-utilities", "simulation"]
exclude = [
    # Documentation not needed in the published crate
    "docs/paper/**",
    "docs/research/**",
    "docs/planning/**",
    "docs/reviewcycle/**",
    "docs/claudetracking/**",
    "docs/claudeguide/**",
    "docs/features/**",
    "docs/vision/**",
    "docs/dev/**",
    "docs/archive/**",
    # Benchmarking assets (keep benchmarking/micro/ for cargo bench)
    "benchmarking/design/**",
    "benchmarking/results/**",
    "benchmarking/scripts/**",
    "benchmarking/downstreamvc/**",
    # CI, scripts, editor config
    ".github/**",
    "scripts/**",
    "CLAUDE.md",
    # Claude agent files
    ".claude/**",
    # Integration tests (not needed in published crate)
    "tests/**",
]

[dependencies]
# Pure Rust bioinformatics I/O (no C dependencies)
noodles-bam = "0.87"
noodles-sam = "0.83"
noodles-fasta = "0.60"
noodles-bgzf = "0.46"
noodles-core = "0.19"

# RNG and distributions
rand = "0.9"
rand_distr = "0.5"

# Parallelism
rayon = "1.10"
crossbeam-channel = "0.5"

# Compression — pure-Rust backend (miniz_oxide) avoids the libz-sys/cmake dependency
flate2 = { version = "1.1", default-features = false, features = ["rust_backend"] }

# CLI
clap = { version = "4", features = ["derive"] }

# Config / serialization
serde = { version = "1", features = ["derive"] }
serde_yaml = "0.9"
serde_json = "1"

# Logging
tracing = "0.1"
tracing-subscriber = { version = "0.3", features = ["env-filter"] }

# Progress
indicatif = "0.18"

# Error handling
anyhow = "1"
noodles-tabix = "0.61"
noodles-csi = "0.55"

[dev-dependencies]
tempfile = "3"
approx = "0.5"
criterion = { version = "0.8", features = ["html_reports"] }

[[bench]]
name = "varforge_benchmarks"
path = "benchmarking/micro/varforge_benchmarks.rs"
harness = false

[profile.release]
lto = "thin"
strip = "symbols"