barcode-count 0.11.1

use anyhow::{Context, Result};
use chrono::Local;
use clap::{crate_version, App, Arg};

/// A struct that contains and initiates all input arguments
pub struct Args {
    pub fastq: String,                           // fastq file path
    pub format: String,                          // format scheme file path
    pub sample_barcodes_option: Option<String>,  // sample barcode file path.  Optional
    pub counted_barcodes_option: Option<String>, // building block barcode file path. Optional
    pub output_dir: String,                      // output directory.  Deafaults to './'
    pub threads: u16, // Number of threads to use.  Defaults to number of threads on the machine
    pub prefix: String, // Prefix string for the output files
    pub merge_output: bool, // Whether or not to create an additional output file that merges all samples
    pub barcodes_errors_option: Option<u16>, // Optional input of how many errors are allowed in each building block barcode.  Defaults to 20% of the length
    pub sample_errors_option: Option<u16>, // Optional input of how many errors are allowed in each sample barcode.  Defaults to 20% of the length
    pub constant_errors_option: Option<u16>, // Optional input of how many errors are allowed in each constant region barcode.  Defaults to 20% of the length
    pub min_average_quality_score: f32,
    pub enrich: bool,
}

impl Args {
    pub fn new() -> Result<Self> {
        let total_cpus = num_cpus::get().to_string();
        let today = Local::now().format("%Y-%m-%d").to_string();
        // parse arguments
        let args = App::new("NGS-Barcode-Count")
        .version(crate_version!())
        .author("Rory Coffey <coffeyrt@gmail.com>")
        .about("Counts barcodes located in sequencing data")
        .arg(
            Arg::with_name("fastq")
                .short("f")
                .long("fastq")
                .takes_value(true)
                .required(true)
                .help("FastQ file"),
        )
        .arg(
            Arg::with_name("format_file")
                .short("q")
                .long("sequence-format")
                .takes_value(true)
                .required(true)
                .help("Sequence format file"),
        )
        .arg(
            Arg::with_name("sample_file")
                .short("s")
                .long("sample-barcodes")
                .takes_value(true)
                .help("Sample barcodes file"),
        )
        .arg(
            Arg::with_name("barcode_file")
                .short("c")
                .long("counted-barcodes")
                .takes_value(true)
                .help("Counted barcodes file"),
        )
        .arg(
            Arg::with_name("threads")
                .short("t")
                .long("threads")
                .takes_value(true)
                .default_value(&total_cpus)
                .help("Number of threads"),
        )
        .arg(
            Arg::with_name("dir")
                .short("o")
                .long("output-dir")
                .takes_value(true)
                .default_value("./")
                .help("Directory to output the counts to"),
        )
        .arg(
            Arg::with_name("prefix")
                .short("p")
                .long("prefix")
                .takes_value(true)
                .default_value(&today)
                .help("File prefix name.  THe output will end with '_<sample_name>_counts.csv'"),
        )
        .arg(
            Arg::with_name("merge-output")
                .short("m")
                .long("merge-output")
                .takes_value(false)
                .help("Merge sample output counts into a single file.  Not necessary when there is only one sample"),
        )
        .arg(
            Arg::with_name("enrich")
                .long("enrich")
                .short("e")
                .takes_value(false)
                .help("Create output files of enrichment for single and double synthons/barcodes"),
        )
        .arg(
            Arg::with_name("max_barcode")
                .long("max-errors-counted-barcode")
                .takes_value(true)
                .help("Maximimum number of sequence errors allowed within each counted barcode. Defaults to 20% of the total."),
        )
        .arg(
            Arg::with_name("max_sample")
                .long("max-errors-sample")
                .takes_value(true)
                .help("Maximimum number of sequence errors allowed within sample barcode. Defaults to 20% of the total."),
        )
        .arg(
            Arg::with_name("max_constant")
                .long("max-errors-constant")
                .takes_value(true)
                .help("Maximimum number of sequence errors allowed within constant region. Defaults to 20% of the total."),
        )
        .arg(
            Arg::with_name("min")
                .long("min-quality")
                .takes_value(true)
                .default_value("0")
                .help("Minimum average read quality score per barcode"),
        )
        .get_matches();

        let sample_barcodes_option;
        if let Some(sample) = args.value_of("sample_file") {
            sample_barcodes_option = Some(sample.to_string())
        } else {
            sample_barcodes_option = None
        }

        let counted_barcodes_option;
        if let Some(barcodes) = args.value_of("barcode_file") {
            counted_barcodes_option = Some(barcodes.to_string())
        } else {
            counted_barcodes_option = None
        }

        let barcodes_errors_option;
        if let Some(barcodes) = args.value_of("max_barcode") {
            barcodes_errors_option = Some(
                barcodes
                    .parse::<u16>()
                    .context("Unable to convert maximum barcode errors to an integer")?,
            )
        } else {
            barcodes_errors_option = None
        }

        let sample_errors_option;
        if let Some(sample) = args.value_of("max_sample") {
            sample_errors_option = Some(
                sample
                    .parse::<u16>()
                    .context("Unable to convert maximum sample errors to an integer")?,
            )
        } else {
            sample_errors_option = None
        }

        let constant_errors_option;
        if let Some(constant) = args.value_of("max_constant") {
            constant_errors_option = Some(
                constant
                    .parse::<u16>()
                    .context("Unable to convert maximum constant errors to an integer")?,
            )
        } else {
            constant_errors_option = None
        }

        let merge_output = args.is_present("merge-output");
        let enrich = args.is_present("enrich");
        let fastq = args.value_of("fastq").unwrap().to_string();
        let format = args.value_of("format_file").unwrap().to_string();
        let output_dir = args.value_of("dir").unwrap().to_string();
        let threads = args
            .value_of("threads")
            .unwrap()
            .parse::<u16>()
            .context("Unable to convert threads to an integer")?;
        let prefix = args.value_of("prefix").unwrap().to_string();
        let min_average_quality_score = args
            .value_of("min")
            .unwrap()
            .parse::<f32>()
            .context("Unable to convert min score to a float")?;

        Ok(Args {
            fastq,
            format,
            sample_barcodes_option,
            counted_barcodes_option,
            output_dir,
            threads,
            prefix,
            merge_output,
            barcodes_errors_option,
            sample_errors_option,
            constant_errors_option,
            min_average_quality_score,
            enrich,
        })
    }
}