readmerger 0.1.0-alpha

Tool for rapidly merging FASTQ files. Never use cat again!
Documentation 
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use clap::Parser;
use readmerger::{
    build_merge_tree, find_fastqs, prepare_for_merges, publish_final_fastq, traverse_tree,
};
use std::io;

#[derive(Parser)]
struct Cli {
    #[clap(value_enum)]
    readdir: String,
    output_name: String,
}

fn main() -> io::Result<()> {
    let args = Cli::parse();
    let input_dir = args.readdir;
    let output_path = args.output_name;

    // find input FASTQ files in the provided directory
    let fastq_files = find_fastqs(&input_dir)
        .expect("Failed to find any FASTQ files in the provided search directory.");

    // determine which files will be appended to while re-compressing with Zstandard
    let prepped_files = prepare_for_merges(fastq_files, &input_dir).expect(
        "FASTQ files could not be read. Please check to make sure they are uncompressed, \
        gzip-compressed, or zstd-compressed.",
    );

    // construct merge tree
    let merge_tree = build_merge_tree(&prepped_files, None)?;
    println!("\n\nMerge tree constructed:\n\n{:#?}\n\n", merge_tree);

    // traverse the tree and merge file pairs until none remain
    traverse_tree(&merge_tree).expect("Merge tree could not be traversed.");

    // publish the final FASTQ
    let final_result = publish_final_fastq(&input_dir, &output_path);

    match final_result {
        Ok(_) => println!("Readmerger completed successfully."),
        Err(message) => panic!("Readmerger encountered this error:\n{}", message),
    }

    Ok(())
}