rosella 0.5.7

Metagenome assembled genome recovery from metagenomes using UMAP and HDBSCAN
Documentation 
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pub mod cli;
pub mod coverage;
pub mod external_command_checker;
pub mod external;
pub mod kmers;
pub mod recover;

// #[cfg(not(feature = "no_flight"))]
pub mod refine;

#[cfg(feature = "no_flight")]
pub mod clustering;
#[cfg(feature = "no_flight")]
pub mod embedding;
#[cfg(feature = "no_flight")]
pub mod graphs;
#[cfg(feature = "no_flight")]
pub mod sketch;

#[macro_use]
extern crate anyhow;

use log::info;
use anyhow::Result;
use std::{path::Path, io::{BufReader, BufRead}};


pub const AUTHOR: &str =
    "Rhys J. P. Newell, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology";
pub const AUTHOR_AND_EMAIL: &str =
    "Rhys J. P. Newell, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology <rhys.newell94 near gmail.com>";
pub const EMAIL: &str = "rhys.newell94 near gmail.com";

pub fn parse_percentage(m: &clap::ArgMatches, parameter: &str) -> f32 {
    match m.contains_id(parameter) {
        true => {
            let mut percentage: f32 = *m.get_one(parameter).unwrap();
            if percentage >= 1.0 && percentage <= 100.0 {
                percentage = percentage / 100.0;
            } else if percentage < 0.0 || percentage > 100.0 {
                panic!("Invalid alignment percentage: '{}'", percentage);
            }
            info!("Using {} {}%", parameter, percentage * 100.0);
            percentage
        }
        false => 0.0,
    }
}

// Enum for exclusion out here so long read can find it
pub enum GenomeExclusionTypes {
    SeparatorType,
    NoneType,
    GenomesAndContigsType,
}

/// read any file into a buffered reader, optionally unzipping it
pub fn get_file_reader<P: AsRef<Path>>(file_path: P) -> Result<Box<dyn BufRead>> {
    let reader = BufReader::new(Box::new(std::fs::File::open(file_path)?));
    Ok(Box::new(reader))
}