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

mod field;

use std::{error, fmt, str::FromStr};

use self::field::Field;

const FIELD_DELIMITER: char = '\t';
const MAX_FIELDS: usize = 6;

/// A FASTQ index record.
#[derive(Debug, Default, Eq, PartialEq)]
pub struct Record {
    name: String,
    len: u64,
    sequence_offset: u64,
    line_bases: u64,
    line_width: u64,
    quality_scores_offset: u64,
}

#[allow(clippy::len_without_is_empty)]
impl Record {
    /// Creates a FASTQ index record.
    pub fn new(
        name: String,
        len: u64,
        sequence_offset: u64,
        line_bases: u64,
        line_width: u64,
        quality_scores_offset: u64,
    ) -> Self {
        Self {
            name,
            len,
            sequence_offset,
            line_bases,
            line_width,
            quality_scores_offset,
        }
    }

    /// Returns the name.
    pub fn name(&self) -> &str {
        &self.name
    }

    /// Returns the length of the sequence.
    pub fn len(&self) -> u64 {
        self.len
    }

    /// Returns the offset to the sequence from the start.
    pub fn sequence_offset(&self) -> u64 {
        self.sequence_offset
    }

    /// Returns the number of bases in the sequence.
    pub fn line_bases(&self) -> u64 {
        self.line_bases
    }

    /// Returns the number of characters in the sequence.
    pub fn line_width(&self) -> u64 {
        self.line_width
    }

    /// Returns the offset to the quality scores from the start.
    pub fn quality_scores_offset(&self) -> u64 {
        self.quality_scores_offset
    }
}

/// An error returned when a raw FASTQ index record fails to parse.
#[derive(Clone, Debug, Eq, PartialEq)]
pub enum ParseError {
    /// The input is empty.
    Empty,
    /// A field is missing.
    Missing(Field),
    /// A field is invalid.
    Invalid(Field, std::num::ParseIntError),
}

impl error::Error for ParseError {}

impl fmt::Display for ParseError {
    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
        match self {
            Self::Empty => f.write_str("empty input"),
            Self::Missing(field) => write!(f, "missing field: {:?}", field),
            Self::Invalid(field, e) => write!(f, "invalid {:?} field: {}", field, e),
        }
    }
}

impl FromStr for Record {
    type Err = ParseError;

    fn from_str(s: &str) -> Result<Self, Self::Err> {
        if s.is_empty() {
            return Err(ParseError::Empty);
        }

        let mut fields = s.splitn(MAX_FIELDS, FIELD_DELIMITER);

        let name = parse_string(&mut fields, Field::Name)?;
        let len = parse_u64(&mut fields, Field::Length)?;
        let sequence_offset = parse_u64(&mut fields, Field::SequenceOffset)?;
        let line_bases = parse_u64(&mut fields, Field::LineBases)?;
        let line_width = parse_u64(&mut fields, Field::LineWidth)?;
        let quality_scores_offset = parse_u64(&mut fields, Field::QualityScoresOffset)?;

        Ok(Self {
            name,
            len,
            sequence_offset,
            line_bases,
            line_width,
            quality_scores_offset,
        })
    }
}

fn parse_string<'a, I>(fields: &mut I, field: Field) -> Result<String, ParseError>
where
    I: Iterator<Item = &'a str>,
{
    fields
        .next()
        .ok_or(ParseError::Missing(field))
        .map(|s| s.into())
}

fn parse_u64<'a, I>(fields: &mut I, field: Field) -> Result<u64, ParseError>
where
    I: Iterator<Item = &'a str>,
{
    fields
        .next()
        .ok_or(ParseError::Missing(field))
        .and_then(|s| s.parse().map_err(|e| ParseError::Invalid(field, e)))
}

#[cfg(test)]
mod tests {
    use super::*;

    #[test]
    fn test_from_str() {
        assert_eq!(
            "r0\t4\t4\t4\t5\t11".parse(),
            Ok(Record::new(String::from("r0"), 4, 4, 4, 5, 11))
        );

        assert_eq!("".parse::<Record>(), Err(ParseError::Empty));

        assert_eq!(
            "r0".parse::<Record>(),
            Err(ParseError::Missing(Field::Length))
        );

        assert!(matches!(
            "r0\tnoodles".parse::<Record>(),
            Err(ParseError::Invalid(Field::Length, _))
        ));
    }
}