genome-sh 0.1.0

The jq of genomics. Fast, local, human-readable variant analysis.
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use std::path::PathBuf;

use anyhow::Result;
use clap::Args;

#[derive(Args)]
pub struct ExtractArgs {
    /// Input CRAM or BAM file.
    pub input: PathBuf,

    /// Reference genome version (GRCh37 or GRCh38).
    #[arg(long, default_value = "GRCh38")]
    pub r#ref: String,

    /// Output file. Defaults to stdout.
    #[arg(short, long)]
    pub output: Option<PathBuf>,

    /// Genomic region to extract (e.g., chr17:43000000-44000000).
    #[arg(long)]
    pub region: Option<String>,

    /// Minimum mapping quality.
    #[arg(long, default_value = "20")]
    pub min_quality: u8,

    /// Minimum read depth at a position to call a variant.
    #[arg(long, default_value = "8")]
    pub min_depth: u32,

    /// Generate an HTML report.
    #[arg(long)]
    pub report: Option<PathBuf>,
}

impl ExtractArgs {
    pub async fn run(self) -> Result<()> {
        eprintln!("Extract command is not yet implemented.");
        eprintln!("This will stream CRAM/BAM files and call variants.");
        Ok(())
    }
}