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

//! VCF header record and components.

pub mod key;
mod parser;
mod value;

pub use self::{key::Key, value::Value};

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

pub(crate) const PREFIX: &str = "##";

/// A generic VCF header record.
#[derive(Clone, Debug, Eq, PartialEq)]
pub struct Record {
    key: Key,
    value: Value,
}

impl Record {
    /// Creates a generic VCF header record.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_vcf::header::{record::{Key, Value}, Record};
    /// let record = Record::new(Key::FileFormat, Value::String(String::from("VCFv4.3")));
    /// ```
    pub fn new(key: Key, value: Value) -> Self {
        Self { key, value }
    }

    /// Returns the key of the record.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_vcf::header::{record::{Key, Value}, Record};
    /// let record = Record::new(Key::FileFormat, Value::String(String::from("VCFv4.3")));
    /// assert_eq!(record.key(), &Key::FileFormat);
    /// ```
    pub fn key(&self) -> &Key {
        &self.key
    }

    /// Returns the value of the record.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_vcf::header::{record::{Key, Value}, Record};
    /// let record = Record::new(Key::FileFormat, Value::String(String::from("VCFv4.3")));
    /// assert_eq!(record.value(), &Value::String(String::from("VCFv4.3")));
    /// ```
    pub fn value(&self) -> &Value {
        &self.value
    }
}

/// An error returned when a raw VCF header record fails to parse.
#[derive(Clone, Debug, Eq, PartialEq)]
pub enum ParseError {
    /// The input is invalid.
    Invalid,
    /// The record key is invalid.
    InvalidKey(key::ParseError),
}

impl error::Error for ParseError {}

impl fmt::Display for ParseError {
    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
        f.write_str("invalid record: ")?;

        match self {
            Self::Invalid => f.write_str("invalid input"),
            Self::InvalidKey(e) => write!(f, "invalid kind: {}", e),
        }
    }
}

impl FromStr for Record {
    type Err = ParseError;

    fn from_str(s: &str) -> Result<Self, Self::Err> {
        let (_, (raw_key, value)) = parser::parse(s).map_err(|_| ParseError::Invalid)?;
        let key = raw_key.parse().map_err(ParseError::InvalidKey)?;
        Ok(Self::new(key, value))
    }
}

impl From<Record> for (Key, Value) {
    fn from(record: Record) -> Self {
        (record.key, record.value)
    }
}

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

    #[test]
    fn test_from_str() {
        let line = "##fileformat=VCFv4.3";

        assert_eq!(
            line.parse(),
            Ok(Record::new(
                Key::FileFormat,
                Value::String(String::from("VCFv4.3"))
            ))
        );

        let line =
            r#"##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">"#;

        assert_eq!(
            line.parse(),
            Ok(Record::new(
                Key::Info,
                Value::Struct(vec![
                    (String::from("ID"), String::from("NS")),
                    (String::from("Number"), String::from("1")),
                    (String::from("Type"), String::from("Integer")),
                    (
                        String::from("Description"),
                        String::from("Number of samples with data"),
                    ),
                ])
            ))
        );

        assert!("".parse::<Record>().is_err());
    }
}