helicase 0.1.1

SIMD-accelerated library for FASTA/FASTQ parsing and bitpacking
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

use super::*;
use crate::config::*;
use crate::dna_format::*;
use crate::input::*;
use std::io;

/// A wrapper for [`FastaParser`] / [`FastqParser`] detecting the format at runtime.
/// Configured via [`ParserOptions`].
///
/// # Example
///
/// ```rust,no_run
/// use helicase::input::*;
/// use helicase::*;
///
/// // set the options of the parser (at compile-time)
/// const CONFIG: Config = ParserOptions::default().config();
///
/// fn main() {
///     let path = "...";
///
///     // create a parser with the desired options
///     let mut parser = FastxParser::<CONFIG>::from_file(&path).expect("Cannot open file");
///
///     // iterate over records
///     while let Some(_event) = parser.next() {
///         let header = parser.get_header();
///         let seq = parser.get_dna_string();
///         // ...
///     }
/// }
/// ```
pub struct FastxParser<'a, const CONFIG: Config>(Box<dyn HelicaseParserIter + 'a>);

impl<'a, const CONFIG: Config, I: InputData<'a> + 'a> FromInputData<'a, I>
    for FastxParser<'a, CONFIG>
{
    fn from_input(input: I) -> io::Result<Self> {
        match input.first_byte() {
            b'>' => Ok(Self(Box::new(FastaParser::<CONFIG, I>::from_input(input)?))),
            b'@' => Ok(Self(Box::new(FastqParser::<CONFIG, I>::from_input(input)?))),
            _ => Err(io::Error::other(
                "Invalid record start, expected '>' or '@'",
            )),
        }
    }
}

impl<'a, const CONFIG: Config> HelicaseParser for FastxParser<'a, CONFIG> {
    #[inline(always)]
    fn format(&self) -> Format {
        self.0.format()
    }

    #[inline(always)]
    fn clear_record(&mut self) {
        self.0.clear_record();
    }

    #[inline(always)]
    fn clear_chunk(&mut self) {
        self.0.clear_chunk();
    }

    #[inline(always)]
    fn get_header(&self) -> &[u8] {
        self.0.get_header()
    }

    #[inline(always)]
    fn get_header_owned(&mut self) -> Vec<u8> {
        self.0.get_header_owned()
    }

    #[inline(always)]
    fn get_quality(&self) -> Option<&[u8]> {
        self.0.get_quality()
    }

    #[inline(always)]
    fn get_quality_owned(&mut self) -> Option<Vec<u8>> {
        self.0.get_quality_owned()
    }

    #[inline(always)]
    fn get_dna_string(&self) -> &[u8] {
        self.0.get_dna_string()
    }

    #[inline(always)]
    fn get_dna_string_owned(&mut self) -> Vec<u8> {
        self.0.get_dna_string_owned()
    }

    #[inline(always)]
    fn get_dna_columnar(&self) -> &ColumnarDNA {
        self.0.get_dna_columnar()
    }

    #[inline(always)]
    fn get_dna_columnar_owned(&mut self) -> ColumnarDNA {
        self.0.get_dna_columnar_owned()
    }

    #[inline(always)]
    fn get_dna_packed(&self) -> &PackedDNA {
        self.0.get_dna_packed()
    }

    #[inline(always)]
    fn get_dna_packed_owned(&mut self) -> PackedDNA {
        self.0.get_dna_packed_owned()
    }

    #[inline(always)]
    fn get_mask_non_actg(&self) -> &BitMask {
        self.0.get_mask_non_actg()
    }

    #[inline(always)]
    fn get_mask_non_actg_owned(&mut self) -> BitMask {
        self.0.get_mask_non_actg_owned()
    }

    #[inline(always)]
    fn get_mask_n(&self) -> &BitMask {
        self.0.get_mask_n()
    }

    #[inline(always)]
    fn get_mask_n_owned(&mut self) -> BitMask {
        self.0.get_mask_n_owned()
    }

    #[inline(always)]
    fn get_dna_len(&self) -> usize {
        self.0.get_dna_len()
    }
}

impl<'a, const CONFIG: Config> Iterator for FastxParser<'a, CONFIG> {
    type Item = Event;

    #[inline(always)]
    fn next(&mut self) -> Option<Self::Item> {
        self.0.next()
    }
}