varforge 0.1.0

Synthetic cancer sequencing test data generator
Documentation 
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# 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 = "2021"
rust-version = "1.74"
name = "varforge"
version = "0.1.0"
build = false
exclude = [
    "docs/paper/**",
    "docs/research/**",
    "docs/planning/**",
    "docs/reviewcycle/**",
    "docs/claudetracking/**",
    "docs/claudeguide/**",
    "docs/features/**",
    "docs/vision/**",
    "docs/dev/**",
    "docs/archive/**",
    "benchmarking/design/**",
    "benchmarking/results/**",
    "benchmarking/scripts/**",
    "benchmarking/downstreamvc/**",
    ".github/**",
    "scripts/**",
    "CLAUDE.md",
    ".claude/**",
    "tests/**",
]
autolib = false
autobins = false
autoexamples = false
autotests = false
autobenches = false
description = "Synthetic cancer sequencing test data generator"
homepage = "https://github.com/trentzz/varforge"
documentation = "https://docs.rs/varforge"
readme = "README.md"
keywords = [
    "bioinformatics",
    "sequencing",
    "cancer",
    "simulation",
    "genomics",
]
categories = [
    "science",
    "command-line-utilities",
    "simulation",
]
license = "MIT"
repository = "https://github.com/trentzz/varforge"

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

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

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

[dependencies.anyhow]
version = "1"

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

[dependencies.crossbeam-channel]
version = "0.5"

[dependencies.flate2]
version = "1.1"
features = ["rust_backend"]
default-features = false

[dependencies.indicatif]
version = "0.18"

[dependencies.noodles-bam]
version = "0.87"

[dependencies.noodles-bgzf]
version = "0.46"

[dependencies.noodles-core]
version = "0.19"

[dependencies.noodles-csi]
version = "0.55"

[dependencies.noodles-fasta]
version = "0.60"

[dependencies.noodles-sam]
version = "0.83"

[dependencies.noodles-tabix]
version = "0.61"

[dependencies.rand]
version = "0.9"

[dependencies.rand_distr]
version = "0.5"

[dependencies.rayon]
version = "1.10"

[dependencies.serde]
version = "1"
features = ["derive"]

[dependencies.serde_json]
version = "1"

[dependencies.serde_yaml]
version = "0.9"

[dependencies.tracing]
version = "0.1"

[dependencies.tracing-subscriber]
version = "0.3"
features = ["env-filter"]

[dev-dependencies.approx]
version = "0.5"

[dev-dependencies.criterion]
version = "0.8"
features = ["html_reports"]

[dev-dependencies.tempfile]
version = "3"

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