bio-seq 0.15.1

Bit packed and well-typed biological sequences
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

use crate::kmer::{REV_2BIT, sealed};
use bitvec::field::BitField;

use crate::{Ba, Bs};

impl sealed::KmerStorage for usize {
    const BITS: usize = usize::BITS as usize;

    type BaN = Ba<1>;

    fn to_bitarray(self) -> Ba<{ (Self::BITS / usize::BITS) as usize }> {
        Self::BaN::new([self])
    }

    fn from_bitslice(bs: &Bs) -> Self {
        debug_assert!(
            bs.len() <= Self::BITS as usize,
            "bitslice larger than kmer storage type"
        );
        bs.load_le()
    }

    fn complement(&mut self, mask: usize) {
        if mask >= Self::BITS as usize {
            *self ^= Self::MAX;
        } else {
            let mask = (1 << mask) - 1;
            *self ^= mask;
        }
    }

    fn shiftr(&mut self, n: u32) {
        *self >>= n;
    }

    fn rev_blocks_2(&mut self) {
        let mut bs = self.swap_bytes().to_le_bytes();

        for b in &mut bs {
            *b = REV_2BIT[*b as usize];
        }

        *self = Self::from_le_bytes(bs);
    }
}

impl sealed::KmerStorage for u64 {
    const BITS: usize = u64::BITS as usize;

    type BaN = Ba<{ (Self::BITS / usize::BITS) as usize }>;

    #[cfg(target_pointer_width = "64")]
    fn to_bitarray(self) -> Self::BaN {
        Self::BaN::new([self.try_into().unwrap()])
    }

    #[cfg(target_pointer_width = "32")]
    fn to_bitarray(self) -> Self::BaN {
        Self::BaN::new([
            (self & 0xFFFFFFFF) as usize,
            ((self >> 32) & 0xFFFFFFFF) as usize,
        ])
    }

    fn from_bitslice(bs: &Bs) -> Self {
        bs.load_le::<Self>()
    }

    fn shiftr(&mut self, n: u32) {
        *self >>= n;
    }

    fn complement(&mut self, mask: usize) {
        if mask >= Self::BITS as usize {
            *self ^= Self::MAX;
        } else {
            *self ^= (1 << mask) - 1;
        }
    }

    fn rev_blocks_2(&mut self) {
        let mut bs = self.swap_bytes().to_le_bytes();

        for b in &mut bs {
            *b = REV_2BIT[*b as usize];
        }

        *self = Self::from_le_bytes(bs);
    }
}

impl sealed::KmerStorage for u128 {
    const BITS: usize = u128::BITS as usize;
    type BaN = Ba<{ (Self::BITS / usize::BITS) as usize }>;

    #[cfg(target_pointer_width = "64")]
    fn to_bitarray(self) -> Self::BaN {
        Self::BaN::new([self as usize, (self >> 64) as usize])
    }

    #[cfg(target_pointer_width = "32")]
    fn to_bitarray(self) -> Self::BaN {
        Self::BaN::new([
            (self & 0xFFFFFFFF) as usize,
            ((self >> 32) & 0xFFFFFFFF) as usize,
            ((self >> 64) & 0xFFFFFFFF) as usize,
            ((self >> 96) & 0xFFFFFFFF) as usize,
        ])
    }

    fn from_bitslice(bs: &Bs) -> Self {
        bs.load_le::<Self>()
    }

    fn shiftr(&mut self, n: u32) {
        *self >>= n;
    }

    fn complement(&mut self, mask: usize) {
        if mask >= Self::BITS as usize {
            *self ^= Self::MAX;
        } else {
            *self ^= (1 << mask) - 1;
        }
    }

    fn rev_blocks_2(&mut self) {
        let mut bs = self.swap_bytes().to_le_bytes();

        for b in &mut bs {
            *b = REV_2BIT[*b as usize];
        }
        *self = Self::from_le_bytes(bs);
    }
}