klassify 0.1.6

Classify chimeric reads based on unique kmer contents
Documentation 
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use crate::utils::SingletonKmers;

use bincode::{config, decode_from_std_read};
use clap::Parser;
use log::info;
use std::collections::HashMap;
use std::fs::File;
use std::io::BufReader;

#[derive(Parser, Debug)]
pub struct InfoArgs {
    /// Bincode file
    pub bincode_file: String,
}

/// Load the bincode file and print some information about it.
pub fn load_kmer_db(bincode_file: &str) -> SingletonKmers {
    let mut reader = BufReader::new(File::open(bincode_file).unwrap());
    let singleton_kmers: SingletonKmers =
        decode_from_std_read(&mut reader, config::standard()).unwrap();
    info!(
        "Loaded singleton kmers (K={}) from `{}`",
        singleton_kmers.kmer_size, bincode_file
    );
    singleton_kmers
}

/// Create mapping between kmer and the file index
pub fn map_kmer_to_file(singleton_kmers: &SingletonKmers) -> HashMap<u64, usize> {
    // Convert to kmer => file index
    let mut kmer_to_file = HashMap::new();
    for (file_index, kmer_set) in singleton_kmers.kmers.iter().enumerate() {
        for &kmer in kmer_set.iter() {
            kmer_to_file.insert(kmer, file_index);
        }
    }
    info!("Mapped kmers to files");
    kmer_to_file
}

pub fn info(bincode_file: &str) {
    let singleton_kmers = load_kmer_db(bincode_file);
    println!("Kmer size: {}", singleton_kmers.kmer_size);
    println!("Number of FASTAs: {}", singleton_kmers.n());
    println!(
        "Number of kmers: {}",
        singleton_kmers.kmers.iter().map(|x| x.len()).sum::<usize>()
    );
    for (i, fasta_file) in singleton_kmers.ids.iter().enumerate() {
        println!(
            "  {}: {} ({} mers)",
            i + 1,
            fasta_file,
            singleton_kmers.kmers[i].len()
        );
    }
}