Struct Gfa 

pub struct Gfa<T: OptFields> {
    pub header: Header,
    pub segments: Vec<Segment<T>>,
    pub paths: Vec<Path>,
    pub links: Option<Vec<Link<T>>>,
    pub containments: Vec<Containment<T>>,
    pub walk: Vec<Walk>,
    pub jumps: Vec<Jump<T>>,
    pub edges: Vec<Edges<T>>,
    pub fragments: Vec<Fragment<T>>,
    pub groups: Vec<Group>,
    pub gaps: Vec<Gap<T>>,
    pub string2index: HashMap<String, usize>,
}

A representation of a GFA file (v1 + v2)

GFA v1 + 1.1/1.2 + v2

Comment: This implementation should be able to parse any kind of GFA file, but has increased memory consumption, since most node ids are stored at Strings which are a minimum of 24 bytes. This is only maintained, since it is not of further use in any of my projects.

Fields

header: Header

segments: Vec<Segment<T>>

paths: Vec<Path>

links: Option<Vec<Link<T>>>

containments: Vec<Containment<T>>

walk: Vec<Walk>

jumps: Vec<Jump<T>>

edges: Vec<Edges<T>>

fragments: Vec<Fragment<T>>

groups: Vec<Group>

gaps: Vec<Gap<T>>

string2index: HashMap<String, usize>

Implementations

impl<T: OptFields> Gfa<T>

pub fn new() -> Self

Graph constructor

Example

use gfa_reader::Gfa;
let graph: Gfa<()> = Gfa::new();

pub fn check_nc(&mut self) -> Option<Vec<usize>>

Check if the nodes in the graph are

• Nodes are present
• Numeric
• Compact
• Start at 1

Returns: - Option<Vec>: Nodes ids in usize (from String) - Option: The minimum node id

pub fn parse_gfa_file(&mut self, file_name: &str, edges: bool)

Read the graph from a file

Example

use gfa_reader::Gfa;
let mut graph = Gfa::new();
graph.parse_gfa_file("/path/to/graph");
´´´

pub fn to_file(self, file_name: &str)

Write the graph to a file

pub fn convert_to_ncgraph(&self, graph: &Gfa<T>) -> NCGfa<T>

Trait Implementations

impl<T: Debug + OptFields> Debug for Gfa<T>

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

Formats the value using the given formatter.