Struct gfatk::gfa::gfa::GFAtk

pub struct GFAtk(pub GFA<usize, OptionalFields>);

A wrapper around GFA from the gfa crate TODO: make GFAtk generic for any segment name, not just usize.

Tuple Fields

0: GFA<usize, OptionalFields>

Implementations

impl GFAtk

pub fn into_ungraph(&self) -> Result<(GFAGraphLookups, GFAungraph)>

Returns a tuple of GFAGraphLookups (a struct of indices/node names) and an undirected GFA graph structure.

pub fn into_digraph(&self) -> Result<(GFAGraphLookups, GFAdigraph)>

Returns a tuple of GFAGraphLookups (a struct of indices/node names) and an directed GFA graph structure.

Most functionality of this binary is on directed graph structures

pub fn print_extract(&self, sequences_to_keep: Vec<usize>)

A method to print a GFA to STDOUT, given a vector of sequence ID’s to keep.

pub fn make_overlaps(&self, extend_length: usize) -> Result<Overlaps>

Returns the overlaps between all the segments in a GFA.

pub fn print_sequences(
    &self,
    subgraph_index_header: Option<String>
) -> Result<()>

The internal function called when gfatk fasta is called.

Prints all segments of the GFA as-is.

fn parse_coverage_opt(opt: &OptFieldVal) -> Result<&f32>

Two internal functions below to parse coverage of a GFA segment.

Used in gfatk stats.

fn get_coverage(&self) -> Result<f32>

pub fn node_seq_len_and_cov(&self, node: usize) -> Result<(usize, f32)>

Return the coverage and sequence length for a segment, given a segment name.

Note segment names are always usize.

pub fn sequence_stats(
    &self,
    genome_type: GenomeType,
    tabular: bool
) -> Result<(f32, f32, usize)>

The internal function called in gfatk stats.

Returns average GC%, average coverage, and total sequence length for a GFA (sub)graph.

pub fn gen_cov_hash(
    &self,
    graph_lookup: &GFAGraphLookups
) -> Result<HashMap<NodeIndex, usize>>

Returns a HashMap of relative coverage of each node (segment) in the GFA.

Relative here indicates that each segment coverage is divided by the lowest coverage node, and rounded.

pub fn from_path_cli(
    &self,
    path: GFAPath,
    link_map: HashMap<String, usize>,
    call: &str,
    fasta_header: Option<&str>
) -> Result<()>

Take a GFAPath and print out the path from a GFA.

Currently implemented requires two loops of the GFA, and storage of the sequences in a HashMap.

pub fn get_path_lines(&self) -> Result<Vec<(&str, String)>>

Parses the P lines in a GFA

Trait Implementations

impl Clone for GFAtk

fn clone(&self) -> GFAtk

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.