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

use crate::prelude::*;

mod reader;
mod std_traits;
#[cfg(test)]
mod test;
mod view_traits;

pub use reader::*;

/// Holds data for a single [Read](https://en.wikipedia.org/wiki/Read_(biology))
/// or [FASTQ](https://en.wikipedia.org/wiki/FASTQ_format) record.
///
/// <div class="warning">
///
/// **Warning**
///
/// If mutating the `sequence` or `quality` fields, the user must ensure they
/// remain the same length.
///
/// </div>
#[derive(Clone, Eq, PartialEq, Hash, Debug, Default)]
pub struct FastQ {
    pub header:   String,
    pub sequence: Nucleotides,
    pub quality:  QualityScores,
}

/// The corresponding immutable view type for [`FastQ`]. See
/// [Views](crate::data#views) for more details.
///
/// <div class="warning">
///
/// **Warning**
///
/// If mutating the `sequence` or `quality` fields, the user must ensure they
/// remain the same length. For example, do not call [`restrict`] on individual
/// fields.
///
/// </div>
///
/// [`restrict`]: Restrict::restrict
#[derive(Clone, Eq, PartialEq, Hash, Debug, Default)]
pub struct FastQView<'a> {
    pub header:   &'a str,
    pub sequence: NucleotidesView<'a>,
    pub quality:  QualityScoresView<'a>,
}

/// The corresponding mutable view type for [`FastQ`]. See
/// [Views](crate::data#views) for more details.
///
/// <div class="warning">
///
/// **Warning**
///
/// If mutating the `sequence` or `quality` fields, the user must ensure they
/// remain the same length. For example, do not call [`restrict`] on individual
/// fields.
///
/// </div>
///
/// [`restrict`]: Restrict::restrict
#[derive(Eq, PartialEq, Hash, Debug)]
pub struct FastQViewMut<'a> {
    pub header:   &'a mut String,
    pub sequence: NucleotidesViewMut<'a>,
    pub quality:  QualityScoresViewMut<'a>,
}

impl FastQ {
    // Conversions and indexing

    /// Creates a new [`FastQ`] empty object.
    #[inline]
    #[must_use]
    pub fn new() -> Self {
        FastQ {
            header:   String::new(),
            sequence: Nucleotides::new(),
            quality:  QualityScores::new(),
        }
    }

    // FastQ-specific methods

    /// Returns the reverse complement of the FASTQ as a new record.
    #[inline]
    #[must_use]
    pub fn to_reverse_complement(&self) -> FastQ {
        FastQ {
            header:   self.header.clone(),
            sequence: self.sequence.to_reverse_complement(),
            quality:  self.quality.to_reverse(),
        }
    }

    /// Computes the reverse complement of the record in-place.
    #[inline]
    pub fn make_reverse_complement(&mut self) {
        self.sequence.make_reverse_complement();
        self.quality.make_reverse();
    }

    /// Clear the FASTQ record so that it is empty.
    #[inline]
    pub fn clear(&mut self) {
        self.sequence.clear();
        self.quality.clear();
    }
}

impl FastQView<'_> {
    // Conversions and indexing

    /// Creates a new [`FastQView`] empty object.
    #[inline]
    #[must_use]
    pub fn new() -> Self {
        FastQView {
            header:   "",
            sequence: NucleotidesView::new(),
            quality:  QualityScoresView::new(),
        }
    }

    // FastQ-specific methods

    /// Returns the reverse complement of the FASTQ as a new record.
    #[inline]
    #[must_use]
    pub fn to_reverse_complement(&self) -> FastQ {
        FastQ {
            header:   self.header.to_string(),
            sequence: self.sequence.to_reverse_complement(),
            quality:  self.quality.to_reverse(),
        }
    }
}

impl FastQViewMut<'_> {
    // No new() exists for FastQViewMut because it is not possible to create an
    // empty &mut String

    // FastQ-specific methods

    /// Returns the reverse complement of the FASTQ as a new record.
    #[inline]
    #[must_use]
    pub fn to_reverse_complement(&self) -> FastQ {
        FastQ {
            header:   (*self.header).clone(),
            sequence: self.sequence.to_reverse_complement(),
            quality:  self.quality.to_reverse(),
        }
    }

    /// Computes the reverse complement of the record in-place.
    #[inline]
    pub fn make_reverse_complement(&mut self) {
        self.sequence.make_reverse_complement();
        self.quality.make_reverse();
    }
}