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
//! SAM header header sort order.

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

/// A SAM header header sort order (`SO`).
#[derive(Clone, Copy, Debug, Eq, PartialEq)]
pub enum SortOrder {
    /// Alignment order is unknown (`unknown`).
    Unknown,
    /// Alignments are not sorted (`unsorted`).
    Unsorted,
    /// Alignments are sorted by read name (`queryname`).
    QueryName,
    /// Alignments are sorted by reference sequence and position (`coordinate`).
    Coordinate,
}

impl AsRef<str> for SortOrder {
    fn as_ref(&self) -> &str {
        match self {
            Self::Unknown => "unknown",
            Self::Unsorted => "unsorted",
            Self::QueryName => "queryname",
            Self::Coordinate => "coordinate",
        }
    }
}

impl Default for SortOrder {
    fn default() -> Self {
        Self::Unknown
    }
}

impl fmt::Display for SortOrder {
    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
        f.write_str(self.as_ref())
    }
}

/// An error returned when a raw SAM header header sort order fails to parse.
#[derive(Clone, Debug, Eq, PartialEq)]
pub enum ParseError {
    /// The input is empty.
    Empty,
    /// The input is invalid.
    Invalid,
}

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::Invalid => f.write_str("invalid input"),
        }
    }
}

impl FromStr for SortOrder {
    type Err = ParseError;

    fn from_str(s: &str) -> Result<Self, Self::Err> {
        match s {
            "" => Err(ParseError::Empty),
            "unknown" => Ok(Self::Unknown),
            "unsorted" => Ok(Self::Unsorted),
            "queryname" => Ok(Self::QueryName),
            "coordinate" => Ok(Self::Coordinate),
            _ => Err(ParseError::Invalid),
        }
    }
}

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

    #[test]
    fn test_default() {
        assert_eq!(SortOrder::default(), SortOrder::Unknown);
    }

    #[test]
    fn test_fmt() {
        assert_eq!(SortOrder::Unknown.to_string(), "unknown");
        assert_eq!(SortOrder::Unsorted.to_string(), "unsorted");
        assert_eq!(SortOrder::QueryName.to_string(), "queryname");
        assert_eq!(SortOrder::Coordinate.to_string(), "coordinate");
    }

    #[test]
    fn test_from_str() {
        assert_eq!("unknown".parse(), Ok(SortOrder::Unknown));
        assert_eq!("unsorted".parse(), Ok(SortOrder::Unsorted));
        assert_eq!("queryname".parse(), Ok(SortOrder::QueryName));
        assert_eq!("coordinate".parse(), Ok(SortOrder::Coordinate));

        assert_eq!("".parse::<SortOrder>(), Err(ParseError::Empty));
        assert_eq!("noodles".parse::<SortOrder>(), Err(ParseError::Invalid));
        assert_eq!("QueryName".parse::<SortOrder>(), Err(ParseError::Invalid));
    }
}