Function wizard_mode

src/wizard.rs:9–180

()

use std::str::FromStr;

pub(crate) async fn wizard_mode() -> Result<Alignoth> {
    println!("Welcome to Alignoth wizard mode 🪄 Let's build your plot interactively.\n");

    let current_dir = std::env::current_dir()?;
    let bam_files: Vec<_> = fs::read_dir(&current_dir)?
        .filter_map(|entry| entry.ok())
        .map(|e| e.path())
        .filter(|p| {
            p.extension()
                .is_some_and(|ext| ext == "bam" || ext == "sam" || ext == "cram")
        })
        .collect();
    let fasta_files: Vec<_> = fs::read_dir(&current_dir)?
        .filter_map(|entry| entry.ok())
        .map(|e| e.path())
        .filter(|p| {
            p.extension()
                .is_some_and(|ext| ext == "fa" || ext == "fasta")
        })
        .collect();
    let vcf_files: Vec<_> = fs::read_dir(&current_dir)?
        .filter_map(|entry| entry.ok())
        .map(|e| e.path())
        .filter(|p| {
            p.file_name().and_then(|n| n.to_str()).is_some_and(|name| {
                name.ends_with(".vcf.gz") || name.ends_with(".bcf") || name.ends_with(".vcf")
            })
        })
        .collect();
    let bed_files: Vec<_> = fs::read_dir(&current_dir)?
        .filter_map(|entry| entry.ok())
        .map(|e| e.path())
        .filter(|p| p.extension().is_some_and(|ext| ext == "bed"))
        .collect();

    let bam_path = if bam_files.is_empty() {
        Text::new("Path to BAM file:").prompt()?
    } else {
        let choices: Vec<_> = bam_files.iter().map(|p| p.display().to_string()).collect();
        Select::new("Select BAM file:", choices).prompt()?
    };

    let reference_path = if fasta_files.is_empty() {
        Text::new("Path to reference FASTA file:").prompt()?
    } else {
        let choices: Vec<_> = fasta_files
            .iter()
            .map(|p| p.display().to_string())
            .collect();
        Select::new("Select reference FASTA file:", choices).prompt()?
    };

    let contigs = get_fasta_contigs(&PathBuf::from(reference_path.clone()))?;
    let target = Select::new("Select target contig/chromosome:", contigs).prompt()?;

    let mut region = match Select::new(
        "Do you want to visualize around a certain position or a specific region?",
        vec!["Around a position", "Region"],