gfa 0.10.1

pub mod name_conversion;
pub mod orientation;
pub mod traits;

pub use self::orientation::*;
pub use self::traits::*;

use crate::{cigar::CIGAR, optfields::*};

use bstr::{BStr, ByteSlice};
#[cfg(feature = "serde1")]
use serde::{Deserialize, Serialize};

/// This module defines the various GFA line types, the GFA object,
/// and some utility functions and types.

/// Simple representation of a parsed GFA file, using a Vec<T> to
/// store each separate GFA line type.
#[derive(Default, Debug, Clone, PartialEq, PartialOrd)]
pub struct GFA<N, T: OptFields> {
    pub header: Header<T>,
    pub segments: Vec<Segment<N, T>>,
    pub links: Vec<Link<N, T>>,
    pub containments: Vec<Containment<N, T>>,
    pub paths: Vec<Path<N, T>>,
}

/// Enum containing the different kinds of GFA lines.
#[derive(Debug, Clone, PartialEq, PartialOrd)]
pub enum Line<N, T: OptFields> {
    Header(Header<T>),
    Segment(Segment<N, T>),
    Link(Link<N, T>),
    Containment(Containment<N, T>),
    Path(Path<N, T>),
}

macro_rules! some_line_fn {
    ($name:ident, $tgt:ty, $variant:path) => {
        impl<N, T: OptFields> Line<N, T> {
            pub fn $name(self) -> Option<$tgt> {
                if let $variant(x) = self {
                    Some(x)
                } else {
                    None
                }
            }
        }
    };
}

some_line_fn!(some_header, Header<T>, Line::Header);
some_line_fn!(some_segment, Segment<N, T>, Line::Segment);
some_line_fn!(some_link, Link<N, T>, Line::Link);
some_line_fn!(some_containment, Containment<N, T>, Line::Containment);
some_line_fn!(some_path, Path<N, T>, Line::Path);

macro_rules! some_line_ref_fn {
    ($name:ident, $tgt:ty, $variant:path) => {
        impl<'a, N, T: OptFields> LineRef<'a, N, T> {
            pub fn $name(self) -> Option<&'a $tgt> {
                if let $variant(x) = self {
                    Some(x)
                } else {
                    None
                }
            }
        }
    };
}

some_line_ref_fn!(some_header, Header<T>, LineRef::Header);
some_line_ref_fn!(some_segment, Segment<N, T>, LineRef::Segment);
some_line_ref_fn!(some_link, Link<N, T>, LineRef::Link);
some_line_ref_fn!(some_containment, Containment<N, T>, LineRef::Containment);
some_line_ref_fn!(some_path, Path<N, T>, LineRef::Path);

#[derive(Debug, Clone, PartialEq, PartialOrd)]
pub enum LineRef<'a, N, T: OptFields> {
    Header(&'a Header<T>),
    Segment(&'a Segment<N, T>),
    Link(&'a Link<N, T>),
    Containment(&'a Containment<N, T>),
    Path(&'a Path<N, T>),
}

impl<N, T: OptFields> GFA<N, T> {
    /// Insert a GFA line (wrapped in the Line enum) into an existing
    /// GFA. Simply pushes it into the corresponding Vec in the GFA,
    /// or replaces the header, so there's no deduplication or sorting
    /// taking place.
    #[inline]
    pub fn insert_line(&mut self, line: Line<N, T>) {
        use Line::*;
        match line {
            Header(h) => self.header = h,
            Segment(s) => self.segments.push(s),
            Link(s) => self.links.push(s),
            Containment(s) => self.containments.push(s),
            Path(s) => self.paths.push(s),
        }
    }

    /// Consume a GFA object to produce an iterator over all the lines
    /// contained within. The iterator first produces all segments, then
    /// links, then containments, and finally paths.
    pub fn lines_into_iter(self) -> impl Iterator<Item = Line<N, T>> {
        use Line::*;
        let segs = self.segments.into_iter().map(Segment);
        let links = self.links.into_iter().map(Link);
        let conts = self.containments.into_iter().map(Containment);
        let paths = self.paths.into_iter().map(Path);

        segs.chain(links).chain(conts).chain(paths)
    }

    /// Return an iterator over references to the lines in the GFA
    pub fn lines_iter(&'_ self) -> impl Iterator<Item = LineRef<'_, N, T>> {
        use LineRef::*;
        let segs = self.segments.iter().map(Segment);
        let links = self.links.iter().map(Link);
        let conts = self.containments.iter().map(Containment);
        let paths = self.paths.iter().map(Path);

        segs.chain(links).chain(conts).chain(paths)
    }
}

impl<N: SegmentId, T: OptFields> GFA<N, T> {
    pub fn new() -> Self {
        Default::default()
    }
}

/// The header line of a GFA graph
#[derive(Debug, Clone, PartialEq, PartialOrd)]
pub struct Header<T: OptFields> {
    pub version: Option<Vec<u8>>,
    pub optional: T,
}

impl<T: OptFields> Default for Header<T> {
    fn default() -> Self {
        Header {
            version: Some("1.0".into()),
            optional: Default::default(),
        }
    }
}

/// A segment in a GFA graph. Generic over the name type, but
/// currently the parser is only defined for N = Vec<u8>
#[derive(Default, Debug, Clone, PartialEq, PartialOrd, Hash)]
#[cfg_attr(feature = "serde1", derive(Serialize, Deserialize))]
pub struct Segment<N, T: OptFields> {
    pub name: N,
    pub sequence: Vec<u8>,
    pub optional: T,
}

impl<T: OptFields> Segment<Vec<u8>, T> {
    #[inline]
    pub fn new(name: &[u8], sequence: &[u8]) -> Self {
        Segment {
            name: Vec::from(name),
            sequence: Vec::from(sequence),
            optional: Default::default(),
        }
    }
}

#[derive(Default, Debug, Clone, PartialEq, PartialOrd, Hash)]
#[cfg_attr(feature = "serde1", derive(Serialize, Deserialize))]
pub struct Link<N, T: OptFields> {
    pub from_segment: N,
    pub from_orient: Orientation,
    pub to_segment: N,
    pub to_orient: Orientation,
    pub overlap: Vec<u8>,
    pub optional: T,
}

impl<T: OptFields> Link<Vec<u8>, T> {
    #[inline]
    pub fn new(
        from_segment: &[u8],
        from_orient: Orientation,
        to_segment: &[u8],
        to_orient: Orientation,
        overlap: &[u8],
    ) -> Link<Vec<u8>, T> {
        Link {
            from_segment: from_segment.into(),
            from_orient,
            to_segment: to_segment.into(),
            to_orient,
            overlap: overlap.into(),
            optional: Default::default(),
        }
    }
}

#[derive(Default, Debug, Clone, PartialEq, PartialOrd, Hash)]
#[cfg_attr(feature = "serde1", derive(Serialize, Deserialize))]
pub struct Containment<N, T: OptFields> {
    pub container_name: N,
    pub container_orient: Orientation,
    pub contained_name: N,
    pub contained_orient: Orientation,
    pub pos: usize,
    pub overlap: Vec<u8>,
    pub optional: T,
}

/// The step list that the path actually consists of is an unparsed
/// Vec<u8> to keep memory down; use path.iter() to get an iterator
/// over the parsed path segments and orientations.
#[derive(Default, Debug, Clone, PartialEq, PartialOrd, Hash)]
#[cfg_attr(feature = "serde1", derive(Serialize, Deserialize))]
pub struct Path<N, T: OptFields> {
    pub path_name: Vec<u8>,
    pub segment_names: Vec<u8>,
    pub overlaps: Vec<Option<CIGAR>>,
    pub optional: T,
    _segment_names: std::marker::PhantomData<N>,
}

impl<N: SegmentId, T: OptFields> Path<N, T> {
    #[inline]
    pub fn new(
        path_name: Vec<u8>,
        segment_names: Vec<u8>,
        overlaps: Vec<Option<CIGAR>>,
        optional: T,
    ) -> Self {
        Path {
            path_name,
            segment_names,
            overlaps,
            optional,
            _segment_names: std::marker::PhantomData,
        }
    }
}

impl<N: SegmentId, T: OptFields> Path<N, T> {
    /// Parses (and copies!) a segment ID in the path segment list
    #[inline]
    fn parse_segment_id(input: &[u8]) -> Option<(N, Orientation)> {
        use Orientation::*;
        let orient = match input.last()? {
            b'+' => Forward,
            b'-' => Backward,
            _ => panic!("Path segment did not include orientation"),
        };
        let seg = &input[..input.len() - 1];
        let id = N::parse_id(seg)?;
        Some((id, orient))
    }
}

impl<T: OptFields> Path<Vec<u8>, T> {
    /// Produces an iterator over the segments of the given path,
    /// parsing the orientation and producing a slice to each segment
    /// name
    #[inline]
    pub fn iter(&self) -> impl Iterator<Item = (&'_ BStr, Orientation)> {
        self.segment_names
            .split_str(b",")
            .filter_map(Self::segment_id_ref)
    }

    fn segment_id_ref(input: &[u8]) -> Option<(&'_ BStr, Orientation)> {
        use Orientation::*;
        let orient = match input.last()? {
            b'+' => Forward,
            b'-' => Backward,
            _ => panic!("Path segment did not include orientation"),
        };
        let seg = &input[..input.len() - 1];
        Some((seg.as_ref(), orient))
    }
}

impl<T: OptFields> Path<usize, T> {
    /// Produces an iterator over the usize segments of the given
    /// path.
    #[inline]
    pub fn iter<'a>(
        &'a self,
    ) -> impl Iterator<Item = (usize, Orientation)> + 'a {
        self.segment_names
            .split_str(b",")
            .filter_map(Self::parse_segment_id)
    }
}

impl<N, T: OptFields> Segment<N, T> {
    pub(crate) fn nameless_clone<M: Default>(&self) -> Segment<M, T> {
        Segment {
            name: Default::default(),
            sequence: self.sequence.clone(),
            optional: self.optional.clone(),
        }
    }
}

impl<N, T: OptFields> Link<N, T> {
    pub(crate) fn nameless_clone<M: Default>(&self) -> Link<M, T> {
        Link {
            from_segment: Default::default(),
            from_orient: self.from_orient,
            to_segment: Default::default(),
            to_orient: self.to_orient,
            overlap: self.overlap.clone(),
            optional: self.optional.clone(),
        }
    }
}

impl<N, T: OptFields> Containment<N, T> {
    pub(crate) fn nameless_clone<M: Default>(&self) -> Containment<M, T> {
        Containment {
            container_name: Default::default(),
            container_orient: self.container_orient,
            contained_name: Default::default(),
            contained_orient: self.contained_orient,
            pos: self.pos,
            overlap: self.overlap.clone(),
            optional: self.optional.clone(),
        }
    }
}

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

    #[test]
    fn path_iter() {
        use Orientation::*;

        let cigars = vec![b"4M", b"5M"]
            .iter()
            .map(|bs| CIGAR::from_bytestring(&bs[..]))
            .collect();

        let path: Path<Vec<u8>, _> =
            Path::new("14".into(), "11+,12-,13+".into(), cigars, ());

        let mut path_iter = path.iter();
        assert_eq!(Some(("11".into(), Forward)), path_iter.next());
        assert_eq!(Some(("12".into(), Backward)), path_iter.next());
        assert_eq!(Some(("13".into(), Forward)), path_iter.next());
        assert_eq!(None, path_iter.next());
    }

    #[test]
    fn gfa_line_ref_iter() {
        let parser: crate::parser::GFAParser<usize, ()> =
            crate::parser::GFAParser::new();
        let gfa = parser.parse_file(&"./test/gfas/lil.gfa").unwrap();
        let gfa_lineref = gfa.lines_iter();

        for line in gfa_lineref {
            let seg = line.some_segment();
            println!("{:?}", seg);
        }
    }
}