fn return_double_extension_filetype(path: &Path, e1: &str) -> Result<String> {

    let stem = path

        .file_stem()

        .and_then(OsStr::to_str)

        .ok_or_else(|| eyre::eyre!("file has no stem"))?;

    let e2 = Path::new(&stem)

        .extension()

        .and_then(OsStr::to_str)

        .ok_or_else(|| eyre::eyre!("file has no other filetype"))?;

    Ok(format!("{e2}.{e1}"))

}

pub fn get_sample_names(path: PathBuf) -> Result<Vec<String>> {

    let extension: &str = Path::new(&path)

        .extension()

        .and_then(OsStr::to_str)

        .ok_or_else(|| eyre!("No filetype in path"))?;

    let extension = match extension {

        "gz" | "bgz" => return_double_extension_filetype(&path, extension)?,

        _ => extension.to_string(),

    let mut ids = vec![];

    match extension.as_str() {

        "vcf.gz" | "vcf" | "bcf" => {

            let bcf = Reader::from_path(path).expect("Error opening file.");

            let header = bcf.header().clone();

            let samples = header.samples();

            for sample in samples {

                let id = std::str::from_utf8(sample)?;

                ids.push(id.to_string());

        "fam" => {

            for line in read_lines(path)?.flatten() {

                let mut split = line.split('\t');

                let id = split

                    .nth(1)

                    .expect("error splitting by column, is the file tab delimited?");

                ids.push(id.to_string());

            }

    Ok(ids)

}

pub fn run(path: PathBuf) -> Result<()> {

    let ids = get_sample_names(path)?;

    for id in ids {

        println!("{id}");

    }

    Ok(())

}

    #[test]

    fn test_extension_filetype() {

        let path = std::path::PathBuf::from("test.vcf.gz");

        let ftype = return_double_extension_filetype(&path, "gz").unwrap();

        assert_eq!(String::from("vcf.gz"), ftype);

    }