1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88

//! Utility functions for simulating random sequences.

use rand::prelude::*;

/// All 20 amino acids.
pub static AMINO_ACIDS: [u8; 20] = [
    b'A', b'C', b'D', b'E', b'F', b'G', b'H', b'I', b'K', b'L',
    b'M', b'N', b'P', b'Q', b'R', b'S', b'T', b'V', b'W', b'Y'
];

/// All 4 nucleotides and the undetermined/placeholder nucleotide.
pub static NUC: [u8; 5] = [
    b'A', b'C', b'G', b'N', b'T'
];

/// Given an input byte string, create a randomly mutated copy and
/// add random suffixes to both strings.
pub fn rand_mutate_suffix<R: Rng>(a: &mut Vec<u8>, k: usize, alpha: &[u8], suffix_len: usize, rng: &mut R) -> Vec<u8> {
    let mut b = rand_mutate(a, k, alpha, rng);
    let a_suffix = rand_str(suffix_len, alpha, rng);
    let b_suffix = rand_str(suffix_len, alpha, rng);
    a.extend_from_slice(&a_suffix);
    b.extend_from_slice(&b_suffix);
    b
}

/// Given an input byte string, create a randomly mutated copy with
/// a single long random insert.
pub fn rand_mutate_insert<R: Rng>(a: &[u8], k: usize, alpha: &[u8], insert_len: usize, rng: &mut R) -> Vec<u8> {
    let b = rand_mutate(a, k, alpha, rng);
    let insert = rand_str(insert_len, alpha, rng);
    let idx = rng.gen_range(1..b.len());
    let mut res = Vec::with_capacity(b.len() + insert_len);
    // insert the long insert string
    res.extend_from_slice(&b[..idx]);
    res.extend_from_slice(&insert);
    res.extend_from_slice(&b[idx..]);
    res
}

/// Given an input byte string, craete a randomly mutated copy.
pub fn rand_mutate<R: Rng>(a: &[u8], k: usize, alpha: &[u8], rng: &mut R) -> Vec<u8> {
    let mut edits = vec![0u8; a.len()];
    let curr_k: usize = rng.gen_range(k * 3 / 4..k + 1);
    let mut idx: Vec<usize> = (0usize..a.len()).collect();
    idx.shuffle(rng);

    // generate edit types
    for i in 0..curr_k {
        edits[idx[i]] = rng.gen_range(1u8..4u8);
    }

    let mut b = vec![];

    for i in 0..a.len() {
        match edits[i] {
            0u8 => { // same
                b.push(a[i]);
            },
            1u8 => { // diff
                let mut iter = alpha.choose_multiple(rng, 2);
                let first = *iter.next().unwrap();
                let second = *iter.next().unwrap();
                b.push(if first == a[i] { second } else { first });
            },
            2u8 => { // insert
                b.push(*alpha.choose(rng).unwrap());
                b.push(a[i]);
            },
            3u8 => (), // delete
            _ => panic!("This should not have been reached!")
        }
    }

    b
}

/// Generate a random string of a certain length, with a certain
/// alphabet.
pub fn rand_str<R: Rng>(length: usize, alpha: &[u8], rng: &mut R) -> Vec<u8> {
    let mut res = vec![0u8; length];

    for i in 0..length {
        res[i] = *alpha.choose(rng).unwrap();
    }

    res
}