finch_lib 0.4.0

An implementation of min-wise independent permutation locality sensitive hashing ('MinHashing') for genomic data and command-line utility for manipulation.
Documentation 
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use std::cmp;

use crate::sketch_schemes::KmerCount;

pub fn cardinality(sketch: &[KmerCount]) -> Result<u64, &'static str> {
    // Other (possibly more accurate) possibilities:
    // "hyper log-log" estimate from lowest value?
    // multiset distribution applied to total count number?
    // "AKMV" approach: http://people.mpi-inf.mpg.de/~rgemulla/publications/beyer07distinct.pdf

    // fast and simple k-minimum value estimate
    // https://research.neustar.biz/2012/07/09/sketch-of-the-day-k-minimum-values/
    if sketch.is_empty() {
        return Ok(0u64);
    }
    Ok(((sketch.len() - 1) as f32
        / (sketch.last().unwrap().hash as f32 / usize::max_value() as f32)) as u64)
}

/// Generates a Vec of numbers of kmers for each coverage level
///
/// For example, a size 1000 sketch of the same genome repeated 5 times (e.g. 5x coverage) should
/// produce a "histogram" like [0, 0, 0, 0, 1000] (assuming no repetative kmers in the genome)
///
pub fn hist(sketch: &[KmerCount]) -> Vec<u64> {
    let mut counts = vec![0u64; 65536];
    let mut max_count: u64 = 0;
    for kmer in sketch {
        max_count = cmp::max(max_count, u64::from(kmer.count));
        counts[kmer.count as usize - 1] += 1;
    }
    counts.truncate(max_count as usize);
    counts
}

#[test]
fn test_hist() {
    let sketch = vec![
        KmerCount {
            hash: 1,
            kmer: vec![],
            count: 1,
            extra_count: 0,
            label: None,
        },
        KmerCount {
            hash: 2,
            kmer: vec![],
            count: 1,
            extra_count: 0,
            label: None,
        },
        KmerCount {
            hash: 3,
            kmer: vec![],
            count: 1,
            extra_count: 0,
            label: None,
        },
    ];

    let hist_data = hist(&sketch);
    assert_eq!(hist_data.len(), 1);
    assert_eq!(hist_data[0], 3);

    let sketch = vec![
        KmerCount {
            hash: 1,
            kmer: vec![],
            count: 4,
            extra_count: 0,
            label: None,
        },
        KmerCount {
            hash: 2,
            kmer: vec![],
            count: 2,
            extra_count: 0,
            label: None,
        },
        KmerCount {
            hash: 3,
            kmer: vec![],
            count: 4,
            extra_count: 0,
            label: None,
        },
        KmerCount {
            hash: 4,
            kmer: vec![],
            count: 3,
            extra_count: 0,
            label: None,
        },
    ];

    let hist_data = hist(&sketch);
    assert_eq!(hist_data.len(), 4);
    assert_eq!(hist_data[0], 0);
    assert_eq!(hist_data[1], 1);
    assert_eq!(hist_data[2], 1);
    assert_eq!(hist_data[3], 2);
}