zoe 0.0.31

A nightly library for viral genomics
Documentation 
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
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175

//! Helper traits/structs for supporting compile time dispatch and type mappings

use crate::{
    kmer::{
        KmerEncoder,
        encoders::{three_bit::ThreeBitKmerEncoder, two_bit::TwoBitKmerEncoder},
    },
    math::Uint,
};
use std::marker::PhantomData;

/// A zero-size struct used to hold both a `MAX_LEN` argument and a
/// [`KmerEncoder`].
///
/// For valid values of `MAX_LEN`, [`SupportedKmerLen`] will be implemented, and
/// will provide the appropriate integer type to use for the encoded k-mer. See
/// [`SupportedKmerLen`] for more details.
pub struct KmerLen<const MAX_LEN: usize, E: KmerEncoder<MAX_LEN>>(PhantomData<E>);

/// Statically guarantees that a max k-mer length is marked as supported for the
/// given [`KmerEncoder`], as well as provides the appropriate integer type.
///
/// Supported max k-mer lengths for [`ThreeBitKmerEncoder`] are:
///
/// - `2`: uses a `u8`
/// - `3..=5`: uses a `u16`
/// - `6..=10`: uses a `u32`
/// - `11..=21`: uses a `u64`
/// - `22..=42`: uses a `u128`
///
/// For a [`TwoBitKmerEncoder`], they are:
///
/// - `2..=4`: uses a `u8`
/// - `5..=8`: uses a `u16`
/// - `9..=16`: uses a `u32`
/// - `17..=32`: uses a `u64`
/// - `33..=64`: uses a `u128`
///
/// This must never be implemented on any [`KmerLen`] where `MAX_LEN > 255`,
/// since [`Kmer`] uses a `u8` to store the k-mer length.
///
/// [`ThreeBitKmerEncoder`]:
///     crate::kmer::encoders::three_bit::ThreeBitKmerEncoder
/// [`Kmer`]: super::Kmer
pub trait SupportedKmerLen {
    /// The integer type used to store the encoded k-mer.
    type T: Uint;
}

/// A macro for implementing [`SupportedKmerLen`].
macro_rules! impl_supported_kmer_len {
    ($encoder:ident, $($max:expr => $type:ty),*) => {
        $(
            impl SupportedKmerLen for KmerLen<$max, $encoder<$max>> {
                type T = $type;
            }
        )*
    }
}

impl_supported_kmer_len! {
    ThreeBitKmerEncoder,
    2 => u8,
    3 => u16,
    4 => u16,
    5 => u16,
    6 => u32,
    7 => u32,
    8 => u32,
    9 => u32,
    10 => u32,
    11 => u64,
    12 => u64,
    13 => u64,
    14 => u64,
    15 => u64,
    16 => u64,
    17 => u64,
    18 => u64,
    19 => u64,
    20 => u64,
    21 => u64,
    22 => u128,
    23 => u128,
    24 => u128,
    25 => u128,
    26 => u128,
    27 => u128,
    28 => u128,
    29 => u128,
    30 => u128,
    31 => u128,
    32 => u128,
    33 => u128,
    34 => u128,
    35 => u128,
    36 => u128,
    37 => u128,
    38 => u128,
    39 => u128,
    40 => u128,
    41 => u128,
    42 => u128
}

impl_supported_kmer_len! {
    TwoBitKmerEncoder,
    2 => u8,
    3 => u8,
    4 => u8,
    5 => u16,
    6 => u16,
    7 => u16,
    8 => u16,
    9 => u32,
    10 => u32,
    11 => u32,
    12 => u32,
    13 => u32,
    14 => u32,
    15 => u32,
    16 => u32,
    17 => u64,
    18 => u64,
    19 => u64,
    20 => u64,
    21 => u64,
    22 => u64,
    23 => u64,
    24 => u64,
    25 => u64,
    26 => u64,
    27 => u64,
    28 => u64,
    29 => u64,
    30 => u64,
    31 => u64,
    32 => u64,
    33 => u128,
    34 => u128,
    35 => u128,
    36 => u128,
    37 => u128,
    38 => u128,
    39 => u128,
    40 => u128,
    41 => u128,
    42 => u128,
    43 => u128,
    44 => u128,
    45 => u128,
    46 => u128,
    47 => u128,
    48 => u128,
    49 => u128,
    50 => u128,
    51 => u128,
    52 => u128,
    53 => u128,
    54 => u128,
    55 => u128,
    56 => u128,
    57 => u128,
    58 => u128,
    59 => u128,
    60 => u128,
    61 => u128,
    62 => u128,
    63 => u128,
    64 => u128
}

/// A type alias for easily getting the encoded k-mer integer type from
/// `MAX_LEN` and the [`KmerEncoder`].
pub(crate) type MaxLenToType<const MAX_LEN: usize, E> = <KmerLen<MAX_LEN, E> as SupportedKmerLen>::T;