lt-fm-index 0.7.1

FM-index using k-mer lookup table for exact pattern matching
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

/**
Type for the position in index.
Two types are supported:
  - `u32`
  - `u64`
*/
#[cfg(feature = "async-io")]
pub trait Position:
    Sized
    + Copy
    + Clone
    + Ord + PartialOrd + Eq + PartialEq
    + Send + Sync
    + std::fmt::Debug
    + std::ops::Div<Output = Self>
    + std::ops::Rem<Output = Self>
    + std::ops::Add<Output = Self>
    + std::ops::AddAssign<Self>
    + std::ops::Sub<Output = Self>
    + std::cmp::PartialOrd
    + bytemuck::Pod
    + bytemuck::Zeroable
    + capwriter::Save
    + capwriter::Load
    + capwriter::AsyncSave
    + capwriter::AsyncLoad
{
    const ZERO: Self;
    const ONE: Self;
    const BITS: u32;
    fn as_u32(self) -> u32;
    fn from_u32(value: u32) -> Self;
    fn as_u64(self) -> u64;
    fn from_u64(value: u64) -> Self;
    fn as_usize(self) -> usize;
    fn from_usize(value: usize) -> Self;
    fn from_i64(value: i64) -> Self;
    fn as_vec_in_range(from: &Self, to: &Self) -> Vec<Self>;
}
#[cfg(not(feature = "async-io"))]
pub trait Position:
    Sized
    + Copy
    + Clone
    + Ord + PartialOrd + Eq + PartialEq
    + Send + Sync
    + std::fmt::Debug
    + std::ops::Div<Output = Self>
    + std::ops::Rem<Output = Self>
    + std::ops::Add<Output = Self>
    + std::ops::AddAssign<Self>
    + std::ops::Sub<Output = Self>
    + std::cmp::PartialOrd
    + bytemuck::Pod
    + bytemuck::Zeroable
    + capwriter::Save
    + capwriter::Load
{
    const ZERO: Self;
    const ONE: Self;
    const BITS: u32;
    fn as_u32(self) -> u32;
    fn from_u32(value: u32) -> Self;
    fn as_u64(self) -> u64;
    fn from_u64(value: u64) -> Self;
    fn as_usize(self) -> usize;
    fn from_usize(value: usize) -> Self;
    fn from_i64(value: i64) -> Self;
    fn as_vec_in_range(from: &Self, to: &Self) -> Vec<Self>;
}

impl Position for u32 {
    const ZERO: Self = 0_u32;
    const ONE: Self = 1_u32;
    const BITS: u32 = Self::BITS;
    #[inline(always)]
    fn as_u32(self) -> u32 {
        self as u32
    }
    #[inline(always)]
    fn from_u32(value: u32) -> Self {
        value as Self
    }
    #[inline(always)]
    fn as_u64(self) -> u64 {
        self as u64
    }
    #[inline(always)]
    fn from_u64(value: u64) -> Self {
        value as Self
    }
    #[inline(always)]
    fn as_usize(self) -> usize {
        self as usize
    }
    #[inline(always)]
    fn from_usize(value: usize) -> Self {
        value as Self
    }
    #[inline(always)]
    fn from_i64(value: i64) -> Self {
        value as Self
    }
    #[inline(always)]
    fn as_vec_in_range(from: &Self, to: &Self) -> Vec<Self> {
        (*from..*to).collect::<Vec<Self>>()
    }
}
impl Position for u64 {
    const ZERO: Self = 0_u64;
    const ONE: Self = 1_u64;
    const BITS: u32 = Self::BITS;
    #[inline(always)]
    fn as_u32(self) -> u32 {
        self as u32
    }
    #[inline(always)]
    fn from_u32(value: u32) -> Self {
        value as Self
    }
    #[inline(always)]
    fn as_u64(self) -> u64 {
        self as u64
    }
    #[inline(always)]
    fn from_u64(value: u64) -> Self {
        value as Self
    }
    #[inline(always)]
    fn as_usize(self) -> usize {
        self as usize
    }
    #[inline(always)]
    fn from_usize(value: usize) -> Self {
        value as Self
    }
    #[inline(always)]
    fn from_i64(value: i64) -> Self {
        value as Self
    }
    #[inline(always)]
    fn as_vec_in_range(from: &Self, to: &Self) -> Vec<Self> {
        (*from..*to).collect::<Vec<Self>>()
    }
}