Struct seq_geom_parser::FragmentGeomDesc

pub struct FragmentGeomDesc {
    pub read1_desc: Vec<GeomPiece>,
    pub read2_desc: Vec<GeomPiece>,
}

This structure holds our representation of the parsed fragment geometry description.

Fields

read1_desc: Vec<GeomPiece>

The sequence of GeomPieces describing read 1 of this fragment in left-to-right order.

read2_desc: Vec<GeomPiece>

The sequence of GeomPieces describing read 2 of this fragment in left-to-right order.

Implementations

impl FragmentGeomDesc

pub fn is_complex_geometry(&self) -> bool

A “complex” geometry is one that contains a FixedSeq piece, and/or a BoundedRange piece

pub fn is_simple_geometry(&self) -> bool

A “simple” geometry is one that contains only fixed length pieces (but doesn’t include any fixed seq segments) and unbounded pieces.

Trait Implementations

impl Debug for FragmentGeomDesc

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Display for FragmentGeomDesc

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Write back a geometry fragment specification as exactly the type of string the parser should accept in the first place. This is the canonical representation of the geometry.

impl<'a> TryFrom<&'a str> for FragmentGeomDesc

fn try_from(arg: &'a str) -> Result<Self, Self::Error>

This is the main entry point to obtain a FragmentGeomDesc structure. This function parses the FGDL description string provided as arg, and returns either Ok(FragGeomDesc), if the parse is succesful or an anyhow::Error if the parsing fails.

Currently, the FGDL makes a structural assumption that is reflected in the way this function works. The description string will describe the fragment geometry for a fragment consisting of a pair of reads (i.e. currently there is no support for single-end reads or fragments containing > 2 reads).

type Error = Error

The type returned in the event of a conversion error.