varforge 0.1.1

Synthetic cancer sequencing test data generator
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37

//! VarForge: synthetic cancer sequencing data generator.
//!
//! Parses the command-line, initialises logging, and dispatches to the
//! selected subcommand.
mod artifacts;
mod cli;
mod core;
mod editor;
mod io;
mod seq_utils;
mod tumour;
mod umi;
mod variants;

use anyhow::Result;
use clap::Parser;

fn main() -> Result<()> {
    let args = cli::Args::parse();

    tracing_subscriber::fmt()
        .with_env_filter(
            tracing_subscriber::EnvFilter::try_from_env("VARFORGE_LOG")
                .unwrap_or_else(|_| tracing_subscriber::EnvFilter::new(args.log_level())),
        )
        .with_writer(std::io::stderr)
        .init();

    let threads = args.threads;
    match args.command {
        cli::Command::Simulate(opts) => cli::simulate::run(opts, threads),
        cli::Command::Validate(opts) => cli::validate::run(opts),
        cli::Command::Edit(opts) => cli::edit::run(opts, threads),
        cli::Command::LearnProfile(opts) => cli::learn_profile::run(opts, threads),
        cli::Command::BenchmarkSuite(opts) => cli::benchmark_suite::run(opts, threads),
    }
}